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GLA-domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   GLA-domain [ 57629]
Superfamily:   GLA-domain [ 57630]
Families:   GLA-domain [ 57631] (6)


Superfamily statistics
Genomes (71) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,073 2,136 18
Proteins 1,072 2,121 18


Functional annotation
General category General
Detailed category General

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 0.00000000000004577 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.000000000001868 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000003249 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.00001018 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000457 Least Informative Direct
Biological Process (BP) primary metabolic process 0.007589 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9334 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) regulation of biological quality 0 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0000005378 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.000001203 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00001321 Moderately Informative Direct
Biological Process (BP) cellular protein modification process 0.0000818 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000301 Moderately Informative Direct
Biological Process (BP) immune system process 0.0003743 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.0006132 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.000787 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.05178 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1785 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.006009 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.002715 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.009126 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 0.05799 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.1467 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.003385 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.1806 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.295 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.001791 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01679 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.5148 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.3629 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.3079 Moderately Informative Inherited
Biological Process (BP) cell communication 0.1519 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.003749 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.3049 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.1836 Moderately Informative Inherited
Biological Process (BP) gene expression 0.00491 Moderately Informative Inherited
Biological Process (BP) peptide metabolic process 0.01295 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to wounding 0 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.00000000000001079 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.00000000000009834 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0000000000007629 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.00000000004214 Informative Direct
Biological Process (BP) negative regulation of cell death 0.00000000005401 Informative Direct
Biological Process (BP) regulation of proteolysis 0.0000000003546 Informative Direct
Biological Process (BP) vesicle-mediated transport 0.000000001123 Informative Direct
Biological Process (BP) regulation of cell differentiation 0.00000001356 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.00000001592 Informative Direct
Biological Process (BP) single-organism membrane organization 0.0000000265 Informative Direct
Biological Process (BP) regulation of transferase activity 0.00000007082 Informative Direct
Biological Process (BP) negative regulation of cellular protein metabolic process 0.0000002028 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.0000004154 Informative Direct
Biological Process (BP) localization of cell 0.0000005913 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.0000006482 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.000001679 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.000001946 Informative Direct
Biological Process (BP) negative regulation of transport 0.000002126 Informative Direct
Biological Process (BP) behavior 0.000002871 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.000004939 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.00002042 Informative Direct
Biological Process (BP) regulation of phosphorylation 0.00002173 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.00002913 Informative Direct
Biological Process (BP) negative regulation of molecular function 0.0000301 Informative Direct
Biological Process (BP) proteolysis 0.00004723 Informative Direct
Biological Process (BP) movement of cell or subcellular component 0.00005369 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00007472 Informative Direct
Biological Process (BP) regulation of protein modification process 0.00008891 Informative Direct
Biological Process (BP) locomotion 0.0001155 Informative Direct
Biological Process (BP) intracellular signal transduction 0.0001358 Informative Direct
Biological Process (BP) single-organism cellular localization 0.0001868 Informative Direct
Biological Process (BP) regulation of protein localization 0.0001882 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.0002022 Informative Direct
Biological Process (BP) phosphorylation 0.0002384 Informative Direct
Biological Process (BP) positive regulation of transport 0.0003587 Informative Direct
Biological Process (BP) regulation of cellular localization 0.0003757 Informative Direct
Biological Process (BP) regulation of secretion 0.000613 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0006223 Informative Direct
Biological Process (BP) regulation of peptide transport 0.0006587 Informative Direct
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.0007171 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0007735 Informative Direct
Biological Process (BP) regulation of system process 0.04612 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.001031 Informative Inherited
Biological Process (BP) regulation of defense response 1 Informative Inherited
Biological Process (BP) regulation of cytokine production 0.02939 Informative Inherited
Biological Process (BP) negative regulation of gene expression 0.003213 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.001578 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.002711 Informative Inherited
Biological Process (BP) positive regulation of signal transduction 0.1763 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.001085 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.01084 Informative Inherited
Biological Process (BP) intracellular transport 0.04451 Informative Inherited
Biological Process (BP) system process 0.2167 Informative Inherited
Biological Process (BP) cellular chemical homeostasis 0.001455 Informative Inherited
Biological Process (BP) regulation of response to wounding 0 Highly Informative Direct
Biological Process (BP) negative regulation of endopeptidase activity 0 Highly Informative Direct
Biological Process (BP) protein maturation 0 Highly Informative Direct
Biological Process (BP) wound healing 0 Highly Informative Direct
Biological Process (BP) leukocyte migration 0 Highly Informative Direct
Biological Process (BP) coagulation 0 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.000000000000007296 Highly Informative Direct
Biological Process (BP) regulation of protein localization to nucleus 0.00000000000002436 Highly Informative Direct
Biological Process (BP) regulation of fibroblast proliferation 0.00000000000002769 Highly Informative Direct
Biological Process (BP) multi-organism cellular process 0.0000000000005775 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 0.000000000001177 Highly Informative Direct
Biological Process (BP) regulation of nucleocytoplasmic transport 0.000000000001538 Highly Informative Direct
Biological Process (BP) negative regulation of hemostasis 0.000000000002308 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase B signaling 0.000000000002354 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.00000000000291 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.00000000000441 Highly Informative Direct
Biological Process (BP) cell chemotaxis 0.000000000004682 Highly Informative Direct
Biological Process (BP) negative regulation of secretion by cell 0.000000000008859 Highly Informative Direct
Biological Process (BP) negative regulation of apoptotic process 0.000000000009166 Highly Informative Direct
Biological Process (BP) activation of protein kinase activity 0.00000000001372 Highly Informative Direct
Biological Process (BP) positive regulation of lymphocyte activation 0.00000000001906 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.0000000000449 Highly Informative Direct
Biological Process (BP) negative regulation of coagulation 0.00000000008935 Highly Informative Direct
Biological Process (BP) regulation of interleukin-1 production 0.000000000096 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.0000000001022 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0000000001491 Highly Informative Direct
Biological Process (BP) phagocytosis 0.000000000799 Highly Informative Direct
Biological Process (BP) response to nutrient levels 0.0000000009833 Highly Informative Direct
Biological Process (BP) endomembrane system organization 0.000000001388 Highly Informative Direct
Biological Process (BP) response to drug 0.000000001598 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0.000000002553 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0.000000002648 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.00000000273 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00000001763 Highly Informative Direct
Biological Process (BP) positive regulation of cellular protein localization 0.00000003788 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 0.0000007433 Highly Informative Direct
Biological Process (BP) biological adhesion 0.0000008656 Highly Informative Direct
Biological Process (BP) regulation of protein import 0.000001266 Highly Informative Direct
Biological Process (BP) negative regulation of peptide secretion 0.000002052 Highly Informative Direct
Biological Process (BP) regulation of hemopoiesis 0.000003351 Highly Informative Direct
Biological Process (BP) positive regulation of intracellular transport 0.000005176 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 0.00001279 Highly Informative Direct
Biological Process (BP) positive regulation of protein transport 0.00005566 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.00006443 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.0001963 Highly Informative Direct
Biological Process (BP) viral process 0.0005582 Highly Informative Direct
Biological Process (BP) negative regulation of cytokine production 0.0006682 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 0.0007343 Highly Informative Direct
Biological Process (BP) negative regulation of defense response 0.0009307 Highly Informative Direct
Biological Process (BP) positive regulation of cell development 0.405 Highly Informative Inherited
Biological Process (BP) hemostasis 0.07886 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.00175 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 8.27e-16 Least Informative Direct
Molecular Function (MF) binding 0.0415 Least Informative Inherited
Molecular Function (MF) metal ion binding 0.000001834 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.000008837 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.002318 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.9517 Moderately Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0 Informative Direct
Molecular Function (MF) peptidase regulator activity 0.00000000000001901 Informative Direct
Molecular Function (MF) enzyme inhibitor activity 0.000000000001695 Informative Direct
Molecular Function (MF) metal ion transmembrane transporter activity 0.00000001546 Informative Direct
Molecular Function (MF) phospholipid binding 0.00000001582 Informative Direct
Molecular Function (MF) passive transmembrane transporter activity 0.00000004962 Informative Direct
Molecular Function (MF) receptor binding 0.0000006943 Informative Direct
Molecular Function (MF) enzyme activator activity 0.0008374 Informative Direct
Molecular Function (MF) serine hydrolase activity 0 Highly Informative Direct
Molecular Function (MF) modified amino acid binding 0 Highly Informative Direct
Molecular Function (MF) cysteine-type endopeptidase regulator activity involved in apoptotic process 0.0000000000001213 Highly Informative Direct
Molecular Function (MF) calcium ion binding 0.0000000000001432 Highly Informative Direct
Molecular Function (MF) gated channel activity 0.000000001894 Highly Informative Direct
Molecular Function (MF) ion channel activity 0.00000001434 Highly Informative Direct
Molecular Function (MF) kinase regulator activity 0.00000003194 Highly Informative Direct
Molecular Function (MF) cysteine-type endopeptidase inhibitor activity 0.00003874 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endomembrane system 0.0001995 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.6434 Moderately Informative Inherited
Cellular Component (CC) Golgi apparatus 0.000000002824 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine endopeptidases0Moderately InformativeDirect
Enzyme Commission (EC)Coagulation factor Xa0Highly InformativeDirect
Enzyme Commission (EC)Coagulation factor IXa0.00000000005175Highly InformativeDirect
Enzyme Commission (EC)Protein C (activated)0.0000000008721Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.000000004129Moderately InformativeDirect
Biological processHemostasis0InformativeDirect
Biological processOsteogenesis0Highly InformativeDirect
Biological processAcute phase0.0000000000004523Highly InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentGolgi apparatus0.0004314Moderately InformativeDirect
Coding sequence diversityPolymorphism0.00003612Moderately InformativeDirect
DomainSignal0Least InformativeDirect
DomainRepeat0.000000002358Least InformativeDirect
DomainEGF-like domain0InformativeDirect
DomainKringle0.00000000001899Highly InformativeDirect
Molecular functionCalcium0Moderately InformativeDirect
Post-translational modificationHydrolase0.0000000000007978Least InformativeDirect
Post-translational modificationProtease0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000002685Moderately InformativeDirect
Post-translational modificationSerine protease0InformativeDirect
Post-translational modificationToxin0.0000000009282InformativeDirect
Post-translational modificationHemostasis impairing toxin0.000000003792Highly InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationGlycoprotein0.0000001064Least InformativeDirect
Post-translational modificationCleavage on pair of basic residues0Moderately InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect
Post-translational modificationZymogen0InformativeDirect
Post-translational modificationSulfation0.00000000005389InformativeDirect
Post-translational modificationGamma-carboxyglutamic acid0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR000294 SSF57630 Protein matches
Abstract

This domain contains post-translational modifications of many glutamate residues by vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla) [PubMed3106112, PubMed2183788]. The GLA domain is responsible for the high-affinity binding of calcium ions. It starts at the N-terminal extremity of the mature form of proteins and ends with a conserved aromatic residue; a conserved Gla-x(3)-Gla-x-Cys motif [PubMed3317405] is found in the middle of the domain which seems to be important for substrate recognition by the carboxylase.

The 3D structure of the Gla domain has been solved [PubMed7713897, PubMed8663165]. Calcium ions induce conformational changes in the Gla domain and are necessary for the Gla domain to fold properly. A common structural feature of functional Gla domains is the clustering of N-terminal hydrophobic residues into a hydrophobic patch that mediates interaction with the cell surface membrane [PubMed8663165].


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-coverage) · Enzyme Commission (EC) · 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 9 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 GLA-domain 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 9 hidden Markov models representing the GLA-domain 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]