9BVM | pdb_00009bvm

Vitamin K-dependent gamma-carboxylase with protein C propeptide and glutamate-rich region and with vitamin K hydroquinone

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth P]		e9bvmP01	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T: Hom_end	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth P]	PF00594	Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain (Gla)	Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain	This domain is responsible for the high-affinity binding of calcium ions. This domain contains post-translational modifications of many glutamate residues by Vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla).	Domain
A	PF22777	Vitamin K-dependent gamma-carboxylase, lumenal domain (VKGC_lumenal_dom)	Vitamin K-dependent gamma-carboxylase, lumenal domain	Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl carboxylase (VKGC) post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamat ...	Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl carboxylase (VKGC) post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase [1]. This entry represents the lumenal domain found in animals and bacteria. This domain is associated with Pfam:PF05090 [1,2].	Domain
A	PF05090	HTTM domain (HTTM)	HTTM domain	This entry represents the HTTM (for horizontally transferred transmembrane) domain found at the N-terminal in metazoan Vitamin K-dependent gamma-carboxylase and in diverse domain architectures in bacterial proteins. This domain shows four transmembra ...	This entry represents the HTTM (for horizontally transferred transmembrane) domain found at the N-terminal in metazoan Vitamin K-dependent gamma-carboxylase and in diverse domain architectures in bacterial proteins. This domain shows four transmembrane regions [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth P]	Activation peptide	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of cellular process negative regulation of programmed cell death multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of response to wounding regulation of coagulation regulation of multicellular organismal process regulation of hemostasis negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis negative regulation of coagulation regulation of wound healing negative regulation of multicellular organismal process regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process positive regulation of endothelial cell development endothelium development positive regulation of biological process cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation regulation of endothelial cell development anatomical structure development positive regulation of cellular process developmental process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation positive regulation of cell development positive regulation of establishment of endothelial barrier tissue development epithelial cell development establishment of endothelial barrier proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region extracellular space
A	Vitamin K-dependent gamma-carboxylase	carboxy-lyase activity lyase activity catalytic activity gamma-glutamyl carboxylase activity carbon-carbon lyase activity vitamin binding binding small molecule binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding cell population proliferation type B pancreatic cell proliferation cellular process multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding cell population proliferation type B pancreatic cell proliferation cellular process epithelial cell proliferation macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process regulation of localization cellular localization regulation of cellular process transport modulation of chemical synaptic transmission signaling negative regulation of biological process negative regulation of transport negative regulation of neurotransmitter transport cell communication localization synaptic signaling regulation of secretion by cell secretion by cell negative regulation of secretion signal release establishment of localization in cell negative regulation of cellular process negative regulation of secretion by cell trans-synaptic signaling regulation of biological process regulation of signaling negative regulation of neurotransmitter secretion neurotransmitter secretion regulation of transport secretion regulation of neurotransmitter transport export from cell cell-cell signaling neurotransmitter transport establishment of localization regulation of secretion chemical synaptic transmission signal release from synapse regulation of trans-synaptic signaling regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of cell communication biosynthetic process gene expression macromolecule biosynthetic process protein maturation developmental process regulation of multicellular organismal development negative regulation of bone development regulation of developmental process negative regulation of developmental process animal organ development regulation of bone development multicellular organism development skeletal system development anatomical structure development regulation of multicellular organismal process negative regulation of multicellular organismal process bone development system development cellular response to stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus vitamin K metabolic process ketone metabolic process chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis regulation of steroid biosynthetic process negative regulation of small molecule metabolic process steroid metabolic process regulation of lipid metabolic process lipid biosynthetic process negative regulation of lipid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process regulation of testosterone biosynthetic process small molecule metabolic process steroid biosynthetic process regulation of biosynthetic process negative regulation of steroid metabolic process negative regulation of testosterone biosynthetic process olefinic compound biosynthetic process small molecule biosynthetic process regulation of ketone biosynthetic process negative regulation of metabolic process regulation of steroid metabolic process regulation of ketone metabolic process testosterone biosynthetic process negative regulation of biosynthetic process negative regulation of steroid biosynthetic process olefinic compound metabolic process regulation of lipid biosynthetic process regulation of metabolic process ketone biosynthetic process negative regulation of lipid metabolic process lipid metabolic process	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth P]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
B [auth P]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B [auth P]	IPR000742	EGF-like domain	Domain
B [auth P]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
B [auth P]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
B [auth P]	IPR050442	Peptidase S1 family, coagulation factors	Family
B [auth P]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth P]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
B [auth P]	IPR001314	Peptidase S1A, chymotrypsin family	Family
B [auth P]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B [auth P]	IPR001254	Serine proteases, trypsin domain	Domain
B [auth P]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
B [auth P]	IPR001881	EGF-like calcium-binding domain	Domain
B [auth P]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
B [auth P]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
A	IPR011020	HTTM-like	Domain
A	IPR053935	Vitamin K-dependent gamma-carboxylase, lumenal domain	Domain
A	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
A	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
A	IPR053934	HTTM domain	Domain
A	IPR007782	Vitamin K-dependent gamma-carboxylase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth P]	Pharos: P04070	thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ovarian cancer
A	Pharos: P38435	vitamin K-dependent clotting factors, combined deficiency of, type 1 body skin hyperlaxity due to vitamin K-dependent coagulation factor deficiency malignant pancreatic neoplasm non-small cell lung carcinoma ovarian carcinoma prostate carcinoma tuberculosis astrocytic tumor blood coagulation disease breast carcinoma gastric cancer heart disease large cell medulloblastoma lymphoplasmacytic lymphoma medulloblastoma vitamin K-dependent clotting factors, combined deficiency of, type 1 body skin hyperlaxity due to vitamin K-dependent coagulation factor deficiency malignant pancreatic neoplasm non-small cell lung carcinoma ovarian carcinoma prostate carcinoma tuberculosis astrocytic tumor blood coagulation disease breast carcinoma gastric cancer heart disease large cell medulloblastoma lymphoplasmacytic lymphoma medulloblastoma osteosarcoma pancreatic ductal adenocarcinoma pseudoxanthoma elasticum-like skin manifestations with retinitis pigmentosa urolithiasis atypical teratoid rhabdoid tumor Warfarin Sensitivity Ehlers-Danlos syndrome gastric carcinoma lung adenocarcinoma malignant ependymoma myocardial infarction ovarian cancer plasma cell myeloma psoriasis vitamin K deficiency hemorrhagic disease autosomal recessive inherited pseudoxanthoma elasticum exocrine pancreatic carcinoma glioblastoma invasive ductal breast carcinoma lung cancer

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth P]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Carboxylases	VKGC vitamin K-dependent gamma-carboxylase (also known as GGCX), apo state

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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