2Q8Y | pdb_00002q8y

Structural insight into the enzymatic mechanism of the phophothreonine lyase

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Phosphothreonine lyase-like	8051665	4007459	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phosphothreonine lyase-like	8090470	3002439	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	VRP3	e2q8yA1	A: a+b two layers	X: Translation initiation factor eIF4e and phosphothreonine lyase (From Topology)	H: Translation initiation factor eIF4e and phosphothreonine lyase (From Topology)	T: Translation initiation factor eIF4e and phosphothreonine lyase	F: VRP3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.2430.10	Alpha Beta	2-Layer Sandwich	Phosphothreonine lyase fold	phosphothreonine lyase	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Mitogen-activated protein kinase 7	enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity MAP kinase activity protein binding kinase binding enzyme binding protein kinase binding mitogen-activated protein kinase binding	developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis developmental process multicellular organismal process regulation of multicellular organismal development regulation of biological process regulation of developmental process blood vessel morphogenesis tube development biological regulation angiogenesis vasculature development regulation of vasculature development circulatory system development anatomical structure morphogenesis multicellular organism development tube morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis anatomical structure development regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development calcineurin-NFAT signaling cascade cellular response to stimulus regulation of cellular process response to stimulus signaling intracellular signal transduction cell communication calcium-mediated signaling intracellular signaling cassette cellular process signal transduction calcineurin-mediated signaling positive regulation of protein metabolic process regulation of protein metabolic process positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process positive regulation of metabolic process metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular developmental process cell differentiation negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response response to external stimulus regulation of inflammatory response response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response embryo development negative regulation of cell adhesion regulation of cell-cell adhesion involved in gastrulation heterotypic cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion regulation of heterotypic cell-cell adhesion cell-cell adhesion involved in gastrulation regulation of cell adhesion embryonic morphogenesis gastrulation negative regulation of heterotypic cell-cell adhesion negative regulation of cell-cell adhesion MAPK cascade adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to chemical response to laminar fluid shear stress cellular response to laminar fluid shear stress response to fluid shear stress cellular response to fluid shear stress intrinsic apoptotic signaling pathway in response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of intracellular signal transduction regulation of intrinsic apoptotic signaling pathway regulation of intracellular signal transduction intrinsic apoptotic signaling pathway negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway response to cytokine response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus negative regulation of endothelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process negative regulation of calcineurin-NFAT signaling cascade regulation of calcineurin-mediated signaling regulation of calcium-mediated signaling regulation of calcineurin-NFAT signaling cascade negative regulation of calcium-mediated signaling negative regulation of calcineurin-mediated signaling positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription muscle cell apoptotic process smooth muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of smooth muscle cell apoptotic process negative regulation of smooth muscle cell apoptotic process negative regulation of muscle cell apoptotic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular membraneless organelle nuclear body membraneless organelle PML body
A	27.5 kDa virulence protein	lyase activity catalytic activity	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR003527	Mitogen-activated protein (MAP) kinase, conserved site	Conserved Site
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR000719	Protein kinase domain	Domain
B	IPR050117	Mitogen-activated protein (MAP) kinase	Family
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR008271	Serine/threonine-protein kinase, active site	Active Site
A	IPR003519	OspF/SpvC	Family
A	IPR038498	OspF/SpvC superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q13164	Hyperalgesia atypical teratoid rhabdoid tumor large cell medulloblastoma medulloblastoma glioblastoma malignant ependymoma primitive neuroectodermal tumor

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048
B	TPO	Parent Component: THR RESID: AA0039 , AA0038 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048 , O-phospho-L-threonine MOD:00047

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.