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TIMP-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   OB-fold [ 50198] (16)
Superfamily:   TIMP-like [ 50242] (3)
Families:   Tissue inhibitor of metalloproteinases, TIMP [ 50243] (2)
  Netrin-like domain (NTR/C345C module) [ 89320] (2)
  The laminin-binding domain of agrin [ 63767]


Superfamily statistics
Genomes (205) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 2,233 5,445 11
Proteins 2,213 5,376 11


Functional annotation
General category Processes_IC
Detailed category Proteases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.00000067690Least InformativeDirect
Biological Process (BP)regulation of cell communication0.0000014250.0000000000002723Moderately InformativeDirect
Biological Process (BP)regulation of signaling0.00000023410.000000000001395Moderately InformativeDirect
Biological Process (BP)regulation of response to stimulus0.000011110Moderately InformativeDirect
Biological Process (BP)regulation of protein metabolic process0.0000077320.000002289Moderately InformativeDirect
Biological Process (BP)regulation of molecular function0.000000001870.00009742Moderately InformativeDirect
Biological Process (BP)negative regulation of metabolic process0.0000017380.6517Moderately InformativeInherited
Biological Process (BP)negative regulation of cellular process0.00000007550.003667Moderately InformativeInherited
Biological Process (BP)regulation of proteolysis0.0000012580.00000000258InformativeDirect
Biological Process (BP)negative regulation of cellular protein metabolic process0.000000015390.000000006055InformativeDirect
Biological Process (BP)regulation of cell proliferation0.0000000036270.0001745InformativeDirect
Biological Process (BP)negative regulation of molecular function0.000005870.000002876InformativeDirect
Biological Process (BP)regulation of hydrolase activity0.00089410.001445InformativeInherited
Molecular Function (MF)binding0.0000000002250.00000000003581Least InformativeDirect
Molecular Function (MF)metal ion binding0.00000000000019310.000000002576Moderately InformativeDirect
Molecular Function (MF)molecular function regulator0.0000000000000013860.000000000000003188Moderately InformativeDirect
Molecular Function (MF)enzyme inhibitor activity00.00001075InformativeDirect
Molecular Function (MF)receptor binding0.0000000000071780.00000000000000397InformativeDirect
Molecular Function (MF)zinc ion binding00.000000000000001615InformativeDirect
Molecular Function (MF)peptidase regulator activity00.0000000000008221InformativeDirect
Cellular Component (CC)extracellular region part0.0000000000000013480Moderately InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 0.000000000001185 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000002204 Least Informative Direct
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.9295 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.5953 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.02551 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) immune system process 0.00001473 Moderately Informative Direct
Biological Process (BP) anatomical structure morphogenesis 0.0002882 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.0000000000002723 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.000000000001395 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0000000008442 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.00001503 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0005225 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000002289 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.00009742 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.005411 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.04964 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.009317 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.9284 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.8824 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.003667 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.7725 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.09741 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.6517 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.06371 Moderately Informative Inherited
Biological Process (BP) cell communication 0.005636 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) tissue development 0.7509 Moderately Informative Inherited
Biological Process (BP) immune effector process 0.00001094 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.00006089 Informative Direct
Biological Process (BP) immune response 0.0001097 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0000602 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.00006745 Informative Direct
Biological Process (BP) negative regulation of signaling 0.00002787 Informative Direct
Biological Process (BP) regulation of proteolysis 0.00000000258 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.000000006055 Informative Direct
Biological Process (BP) regulation of growth 0.000003625 Informative Direct
Biological Process (BP) locomotion 0.000002701 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0001745 Informative Direct
Biological Process (BP) regulation of phosphorylation 0.0000007031 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.000002876 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.00002099 Informative Direct
Biological Process (BP) generation of neurons 0.000000000001079 Informative Direct
Biological Process (BP) regulation of anatomical structure size 0.00004666 Informative Direct
Biological Process (BP) cell development 0.2598 Informative Inherited
Biological Process (BP) embryo development 0.1486 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.001445 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.002069 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.6817 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.01028 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.00358 Informative Inherited
Biological Process (BP) regulation of defense response 0.2891 Informative Inherited
Biological Process (BP) regulation of immune response 0.6712 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.001202 Informative Inherited
Biological Process (BP) central nervous system development 0.01648 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.1837 Informative Inherited
Biological Process (BP) regulation of lipid metabolic process 0.04854 Informative Inherited
Biological Process (BP) positive regulation of transport 0.1109 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.8733 Informative Inherited
Biological Process (BP) localization of cell 0.00906 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.7888 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.01458 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.02115 Informative Inherited
Biological Process (BP) epithelium development 0.008971 Informative Inherited
Biological Process (BP) regulation of protein modification process 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.001067 Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.00000382 Highly Informative Direct
Biological Process (BP) regulation of cell growth 0.000008262 Highly Informative Direct
Biological Process (BP) morphogenesis of an epithelium 0.0000000002463 Highly Informative Direct
Biological Process (BP) regulation of acute inflammatory response 0.0001368 Highly Informative Direct
Biological Process (BP) regulation of humoral immune response 0.000009023 Highly Informative Direct
Biological Process (BP) small GTPase mediated signal transduction 0.00006827 Highly Informative Direct
Biological Process (BP) regulation of cell size 0.00000000002763 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.0004755 Highly Informative Direct
Biological Process (BP) negative regulation of endopeptidase activity 0.00001325 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.00003582 Highly Informative Direct
Biological Process (BP) forebrain development 0.0003891 Highly Informative Direct
Biological Process (BP) response to estrogen 0.0000001238 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.0009339 Highly Informative Direct
Biological Process (BP) embryonic organ development 0.0009933 Highly Informative Direct
Biological Process (BP) regulation of developmental growth 0.00002506 Highly Informative Direct
Biological Process (BP) neuron development 0.0001357 Highly Informative Direct
Biological Process (BP) regulation of transmembrane receptor protein serine/threonine kinase signaling pathway 0.00001174 Highly Informative Direct
Biological Process (BP) regulation of cellular response to growth factor stimulus 0.0000000001695 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.00000000009018 Highly Informative Direct
Biological Process (BP) regulation of lipid localization 0.0006974 Highly Informative Direct
Biological Process (BP) sensory organ morphogenesis 0.04258 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.01113 Highly Informative Inherited
Biological Process (BP) regulation of G-protein coupled receptor protein signaling pathway 0.01638 Highly Informative Inherited
Biological Process (BP) camera-type eye development 0.06631 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.01208 Highly Informative Inherited
Biological Process (BP) regulation of protein processing 0.09454 Highly Informative Inherited
Biological Process (BP) cell-cell signaling 0.01012 Highly Informative Inherited
Biological Process (BP) cell projection assembly 0.009277 Highly Informative Inherited
Molecular Function (MF) binding 0.00000000003581 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) metal ion binding 0.000000002576 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.000000000000003188 Moderately Informative Direct
Molecular Function (MF) anion binding 1 Moderately Informative Inherited
Molecular Function (MF) carbohydrate derivative binding 0.1856 Moderately Informative Inherited
Molecular Function (MF) enzyme inhibitor activity 0.00001075 Informative Direct
Molecular Function (MF) receptor binding 0.00000000000000397 Informative Direct
Molecular Function (MF) zinc ion binding 0.000000000000001615 Informative Direct
Molecular Function (MF) peptidase regulator activity 0.0000000000008221 Informative Direct
Molecular Function (MF) sulfur compound binding 0.0002036 Informative Direct
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.002114 Informative Inherited
Molecular Function (MF) heparin binding 0.000002259 Highly Informative Direct
Molecular Function (MF) serine hydrolase activity 0.000004183 Highly Informative Direct
Molecular Function (MF) G-protein coupled receptor binding 0.01138 Highly Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) vesicle 0.1242 Moderately Informative Inherited
Cellular Component (CC) extracellular organelle 0.001604 Informative Inherited
Cellular Component (CC) extracellular matrix component 0.0005807 Highly Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0Moderately InformativeDirect
Biological processImmunity0Moderately InformativeDirect
Biological processInflammatory response0InformativeDirect
Biological processInnate immunity0InformativeDirect
Biological processWnt signaling pathway0InformativeDirect
Biological processComplement pathway0Highly InformativeDirect
Biological processComplement alternate pathway0.000000000001767Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.00005314Moderately InformativeDirect
Cellular componentExtracellular matrix0.000000000004789InformativeDirect
Cellular componentSynapse0.00000003342InformativeDirect
DomainSignal0Least InformativeDirect
DomainLaminin EGF-like domain0Highly InformativeDirect
Molecular functionZinc0.0000000000223Least InformativeDirect
Post-translational modificationDevelopmental protein0Moderately InformativeDirect
Post-translational modificationProtease inhibitor0InformativeDirect
Post-translational modificationToxin0.002328InformativeInherited
Post-translational modificationMetalloenzyme inhibitor0Highly InformativeDirect
Post-translational modificationGrowth factor8.797e-16Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0.0000000000005673Moderately InformativeDirect
Post-translational modificationSulfation0.000007566InformativeDirect
Post-translational modificationThioester bond0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008993 SSF50242 Protein matches
Abstract

Tissue inhibitors of metalloproteinases (TIMP) are a family of proteins that can form complexes with extracellular matrix metalloproteinases (such as collagenases) and irreversibly inactivate them [PubMed2793861]. TIMP and related proteins contains a five-stranded antiparallel beta-sheet that is rolled over on itself to form a closed beta-barrel, and two short helices, which pack close to one another on the same barrel face. A comparison of the delta TIMP-2 structure with other known protein folds reveals that the beta-barrel topology is homologous to that seen in proteins of the oligosaccharide/oligonucleotide binding (OB) fold family, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha-helix located between the third and fourth strands [PubMed7918391].

Other proteins contain domains with a similar OB-like fold:

  • Netrin-like domain (NTR/C345C module), found in procollagen c-proteinase enhancer protein PCOLCE, and in the complement C5 domain.
  • Laminin-binding domain, found in agrin.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 6 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a TIMP-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 6 hidden Markov models representing the TIMP-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · UniProtKB KeyWords (KW) · Internal database links ]