A List of types of proteins is part of on-going attempts to manage the large amounts of information concerning gene

Gene

A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

s and protein

Protein

Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

s. Gene sequencing efforts and genome

Genome

In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....

 sequencing projects have led to the creation of many gene databases and attempts to organize all of the available information. Classifications may be based on structure

Protein structure

Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...

 as in CATH

CATH

The CATH Protein Structure Classification is a semi-automatic, hierarchical classification of protein domains published in 1997 by Christine Orengo, Janet Thornton and their colleagues....

 and SCOP

SCOP

SCOP may refer to:* Structural Classification of Proteins* Suprachiasmatic nucleus circadian oscillatory protein, a member of the leucine-rich repeat protein family* Société coopérative, a type of corporation in France...

.

The List of types of proteins (on this page, below) is based on the biological categories described in the GO Slims list for "GOA and whole proteome analysis" (format-version: 1.0 date: 17:08:2005 14:57). Modifications are being made as needed, but an effort is being made to keep these "top level" categories limited in number:Note: the original [ftp://ftp.geneontology.org/pub/go/GO_slims/goslim_goa.obo GOA and whole proteome analysis slim] contains many suggested “synonyms” and subcategories for the following categories.

Note: There is also a List of proteins. Specific proteins may be listed there. This page (see below) is for descriptions of types of proteins.

biological process unknown

"Used for the annotation of gene products whose process is not known or cannot be inferred."

Proteins with no known biological function can be categorized according to protein structural criteria (distinctive structural domains), source organism or subcellular location.

Structural categories

Proteins with unknown functions can sometimes be categorized according to their structural features if they contain a recognizable protein domain.

• See Protein domains.

organism

Taxonomy

Taxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...

 categories

If the only thing known about a protein is the organism that produces it, then it can (as a last resort) be categorized according to organism.

• NCBI Taxonomy Browser
• WikiSpecies taxonomy system

cellular component

"The part of a cell of which a gene product is a component; for purpose of GO includes the extracellular environment of cells; a gene product may be a component of one or more parts of a cell; this term includes gene products that are parts of macromolecular complexes\, by the definition that all members of a complex normally copurify under all except extreme conditions."

unlocalized protein complex

"Used as a holding place for cellular components whose precise localization is\, as yet\, unknown\, or has not been determined by GO (the latter is the major reason for nodes to have this parent); this term should not be used for annotation of gene products." See also the cellular component term 'cellular component unknown’ (below).

cellular component unknown

"Used for the annotation of gene products whose localization is not known or cannot be inferred." Consider placing such proteins in Structural categories or organism categories

Cell

Cell (biology)

The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....

"The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope."

cell surface

"The external part of the cell wall

Cell wall

The cell wall is the tough, usually flexible but sometimes fairly rigid layer that surrounds some types of cells. It is located outside the cell membrane and provides these cells with structural support and protection, and also acts as a filtering mechanism. A major function of the cell wall is to...

 and/or cell membrane

Cell membrane

The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells. It basically protects the cell...

."

comment: Note that this term is intended to annotate gene products that are attached to the plasma membrane or cell wall.

2 types of membrane protein

Membrane protein

A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes.-Function:...

s are "integral

Integral membrane protein

An integral membrane protein is a protein molecule that is permanently attached to the biological membrane. Proteins that cross the membrane are surrounded by "annular" lipids, which are defined as lipids that are in direct contact with a membrane protein...

" (such as ion channel

Ion channel

Ion channels are pore-forming proteins that help establish and control the small voltage gradient across the plasma membrane of cells by allowing the flow of ions down their electrochemical gradient. They are present in the membranes that surround all biological cells...

s) and "peripheral

Peripheral membrane protein

Peripheral membrane proteins are proteins that adhere only temporarily to the biological membrane with which they are associated. These molecules attach to integral membrane proteins, or penetrate the peripheral regions of the lipid bilayer. The regulatory protein subunits of many ion channels and...

"

intracellular

Intracellular

Not to be confused with intercellular, meaning "between cells".In cell biology, molecular biology and related fields, the word intracellular means "inside the cell".It is used in contrast to extracellular...

exact_synonym: "protoplasm

Protoplasm

Protoplasm is the living contents of a cell that is surrounded by a plasma membrane. It is a general term of the Cytoplasm . Protoplasm is composed of a mixture of small molecules such as ions, amino acids, monosaccharides and water, and macromolecules such as nucleic acids, proteins, lipids and...

"

"The living contents of a cell; the matter contained within (but not including) the plasma membrane\, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm."

See the Organelles category of Wikipedia.

nucleus

Cell nucleus

In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...

"A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells\, the nucleus contains all of the cell's chromosomes except the organellar chromosomes\, and is the site of RNA synthesis and processing. In some species\, or in specialized cell types\, RNA metabolism or DNA replication may be absent."

Membrane

Biological membrane

A biological membrane or biomembrane is an enclosing or separatingmembrane that acts as a selective barrier, within or around a cell. It consists of a lipid bilayer with embedded proteins that may constitute close to 50% of membrane content...

exact_synonym: "membrane organelle"

"Double layer of lipid molecules that encloses all cells\, and\, in eukaryotes\, many organelles; may be a single or double lipid bilayer; also includes associated proteins."
.
See the Membrane biology category of wikipedia.

See the Membrane proteins category of wikipedia.

See the Integral membrane proteins category of Wikipedia.

chromosome

Chromosome

A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...

"A structure composed of a very long molecular of DNA and associated proteins (e.g. histones) that carries hereditary information."

extracellular

Extracellular

In cell biology, molecular biology and related fields, the word extracellular means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid...

 region

exact_synonym: "extracellular"

Note that this term is intended to annotate gene products that are not attached to the cell surface.

"The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite."

external encapsulating structure

"A structure that lies outside the plasma membrane and surrounds the entire cell."

extracellular space

"That part of a multicellular organism outside the cells proper\, usually taken to be outside the plasma membranes\, and occupied by fluid."

Molecular function

"Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions."

Note: the next four categories (below) are general default categories. Try to find more specific functional categories (further below) for proteins than these general categories.

physiological process

“Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms."...

biological process

"A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products."

cellular process

"Processes that are carried out at the cellular level\, but are not necessarily restricted to a single cell. For example\, cell communication occurs among more than one cell\, but occurs at the cellular level."

catalytic activity

related_synonym: "Enzyme

Enzyme

Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...

 activity"

"Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates

Substrate (biochemistry)

In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...

, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates

Active site

In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...

\, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme

Ribozyme

A ribozyme is an RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA enzyme or catalytic RNA. Many natural ribozymes catalyze either the hydrolysis of one of their own...

) is often also regarded as enzymatic."

Note: see the Wikipedia enzymes category.

aromatase

Aromatase

Aromatase is an enzyme responsible for a key step in the biosynthesis of estrogens. It is a member of the cytochrome P450 superfamily , which are monooxygenases that catalyze many reactions involved in steroidogenesis. In particular, aromatase is responsible for the aromatization of androgens into...

 activity

exact_synonym: "estrogen synthetase"

"Catalysis of the reaction\: R-H + reduced flavoprotein + O2 = R-OH + oxidized flavoprotein + H2O."

• See the Wikipedia EC 1.14.14 category.

motor activity

Catalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate. Also includes prokaryotic motors.

Note: the myosin

Myosin

Myosins comprise a family of ATP-dependent motor proteins and are best known for their role in muscle contraction and their involvement in a wide range of other eukaryotic motility processes. They are responsible for actin-based motility. The term was originally used to describe a group of similar...

, kinesin

Kinesin

A kinesin is a protein belonging to a class of motor proteins found in eukaryotic cells. Kinesins move along microtubule filaments, and are powered by the hydrolysis of ATP . The active movement of kinesins supports several cellular functions including mitosis, meiosis and transport of cellular...

 and Dynein

Dynein

Dynein is a motor protein in cells which converts the chemical energy contained in ATP into the mechanical energy of movement. Dynein transports various cellular cargo by "walking" along cytoskeletal microtubules towards the minus-end of the microtubule, which is usually oriented towards the cell...

 motor proteins are also in the cytoskeleton category.

See the Wikipedia Motor protein article and the motor proteins category of Wikipedia.

helicase

Helicase

Helicases are a class of enzymes vital to all living organisms. They are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separating two annealed nucleic acid strands using energy derived from ATP hydrolysis.-Function:Many cellular processes Helicases are a...

 activity

"Catalysis of the unwinding of a DNA or RNA duplex."

• dnaB
• recQ

integrase

Integrase

Retroviral integrase is an enzyme produced by a retrovirus that enables its genetic material to be integrated into the DNA of the infected cell...

 activity

"Catalysis of the integration of DNA possibly by forming a transient DNA-protein link."

antioxidant activity

"Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage."

metabolism

"Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.

macromolecule metabolism

The chemical reactions involving macromolecules (large molecules including proteins, nucleic acids and carbohydrates. See also: #catabolism.

Proteolysis

Proteolysis

Proteolysis is the directed degradation of proteins by cellular enzymes called proteases or by intramolecular digestion.-Purposes:Proteolysis is used by the cell for several purposes...

• Protease
  Protease
  A protease is any enzyme that conducts proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein....
  
  
  • :Category:EC 3.4

• Protease inhibitor
  Protease inhibitor (biology)
  In biology and biochemistry, protease inhibitors are molecules that inhibit the function of proteases. Many naturally occurring protease inhibitors are proteins....
  
  s
  • Serine protease inhibitors category

amino acid and derivative metabolism

"The chemical reactions involving amino acids, organic acids containing one or more amino substituents\, and compounds derived from amino acids."

nucleobase, nucleoside, nucleotide and nucleic acid metabolism

"The chemical reactions involving nucleobases\, nucleosides\, nucleotides and nucleic acids."

biosynthesis

"The energy-requiring part of metabolism in which simpler substances are transformed into more complex ones\, as in growth and other biosynthetic processes."

catabolism

exact_synonym: "breakdown"

exact_synonym: "degradation"

"Any metabolic process involving the breakdown of complex substances into smaller products\, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism."

Note: use #macromolecule metabolism (above) for proteins, nucleic acids and carbohydrates.

kinase activity

"Catalysis of the transfer of a phosphate group\, usually from ATP\, to a substrate molecule."

oxidoreductase activity

"Catalysis of an oxidation-reduction (redox) reaction\, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized\, while the other acts as hydrogen or electron acceptor and becomes reduced."

transferase activity

"Catalysis of the transfer of a group\, e.g. a methyl group\, glycosyl group\, acyl group\, phosphorus-containing\, or other groups\, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2."

hydrolase activity

"Catalysis of the hydrolysis of various bonds\, e.g. C-O\, C-N\, C-C\, phosphoric anhydride bonds\, etc. Hydrolase is the systematic name for any enzyme of EC class 3."

lyase activity

"Catalysis of the cleavage of C-C\, C-O\, C-N and other bonds by other means than by hydrolysis or oxidation\, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction\, but only one in the other direction. When acting on the single substrate\, a molecule is eliminated and this generates either a new double bond or a new ring." (EC:4)

isomerase activity

"Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5."

ligase activity

"Catalysis of the ligation of two substances with concomitant breaking of a diphosphate linkage\, usually in a nucleoside triphosphate. Ligase is the systematic name for any enzyme of EC class 6."

enzyme regulator activity

"Modulates the activity of an enzyme."

exact_synonym: "enzyme modulator"

signal transducer activity

namespace: molecular_function
def: "Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell."

structural molecule activity

"The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cellphone."

Cytoskeleton

Cytoskeleton

The cytoskeleton is a cellular "scaffolding" or "skeleton" contained within a cell's cytoplasm and is made out of protein. The cytoskeleton is present in all cells; it was once thought to be unique to eukaryotes, but recent research has identified the prokaryotic cytoskeleton...

The cytoskeleton is composed of protein filaments in the cytoplasm.

• The Wikipedia Cytoskeleton category.

extracellular matrix

"A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. As in\, but not restricted to\, the multicellular animals.

binding

"The selective\, often stoichiometric interaction of a molecule with one or more specific sites on another molecule." For ligands that bind to signal transducing receptors\, consider the molecular function term 'receptor binding' (receptor activity, below)

Receptor

Receptor (biochemistry)

In biochemistry, a receptor is a molecule found on the surface of a cell, which receives specific chemical signals from neighbouring cells or the wider environment within an organism...

 activity

"Combining with an extracellular or intracellular messenger to initiate a change in cell activity."

The Wikipedia Receptors category.

protein binding

"Interacting selectively with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules)."

lipid

Lipid

Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, triglycerides, phospholipids, and others...

 binding

"Interacting selectively and non-covalently with a lipid." (GO:0008289)

• Lipid transfer proteins
  Lipid transfer proteins
  Plant lipid transfer proteins, also known as plant LTPs or PLTPs, are a group of highly-conserved proteins of about 9kDa found in higher plant tissues. As its name implies, lipid transfer proteins are responsible for the shuttling of phospholipids and other fatty acid groups between cell membranes...
  
  

cell motility

"Any process involved in the controlled movement of a cell."

exact_synonym: "cell locomotion"

exact_synonym: "cell movement"
Note: also see #motor activity (above) for other proteins involved in cell motility.

cell communication

"Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell\, between a cell and an extracellular matrix\, or between a cell and any other aspect of its environment."

regulation of biological process

"Any process that modulates the frequency\, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression\, protein modification or interaction with a protein or substrate molecule."

development

"The biological process specifically aimed at the progression of an organism over time from an initial condition (e.g. a zygote\, a young adult or a young single celled organism) to a later condition (e.g. a multicellular animal\, an aged adult or a mature single celled organism)." ('developmental process').

cell differentiation

"The process whereby relatively unspecialized cells\, e.g. embryonic or regenerative cells\, acquire specialized structural and/or functional features that characterize the cells\, tissues\, or organs of the mature organism or some other relatively stable phase of the organism's life history."

response to stimulus

"A change in state or activity of a cell or organism (in terms of movement\, secretion\, enzyme production\, gene expression\, etc.) as a result of the perception of a stimulus."

behavior

"The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions."

cell death

"The specific activation or halting of processes within a cell so that its vital functions markedly cease\, rather than simply deteriorating gradually over time\, which culminates in cell death."

transport

"The directed movement of substances (such as macromolecules\, small molecules\, ions) into\, out of\, within or between cells."

protein transporter activity

"Enables the directed movement of proteins into\, out of\, within or between cells."

Nuclear transport

• importin
  Importin
  Importin is a type of protein that moves other protein molecules into the nucleus by binding to a specific recognition sequence, called the nuclear localization signal . Importin is classified as a karyopherin....
  
  , nuclear transport factor 2 (NTF2), Ran
  Ran
  -Organizations:* Rainforest Action Network* Russian Academy of Sciences * The Royal Australian Navy-People:* Nissim of Gerona, Rabbi Nissim ben Reuven...
  
  , exportin

ion transporter activity

"Enables the directed movement of charged atoms or small charged molecules into\, out of\, within or between cells."

channel or pore class transporter activity

"Allows facilitated diffusion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without a carrier-mediated mechanism. They do not exhibit stereospecificity but may be specific for a particular molecular species or class of molecules."

carrier activity

exact synonym: "carrier type transporter"

"Catalysis of the transfer of a specific substance or related group of substances from one side of the membrane to the other."

permease activity

"Catalysis of the stereospecific transfer of a substrate across a biological membrane."

electron transporter activity

"Enables the directed movement of electrons into\, out of\, within or between cells."xqs

electron transport

"The transport of electrons from an electron donor to an electron acceptor." (electron transfer)

pathogenesis

"The specific processes that generate the ability of an organism to cause disease in another."

comment: Note that this term should not be used to annotate gene products that are involved in the host response to pathogenesis. It should only be used to annotate those gene products involved in the generation of pathogenesis by the pathogen itself (virulence).

transcription regulator activity

"Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor

Transcription factor

In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...

."