2GTR | pdb_00002gtr

Human chromodomain Y-like protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d2gtrc_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Crotonase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2gtrb_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Crotonase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2gtra_	Alpha and beta proteins (a/b)	ClpP/crotonase	ClpP/crotonase	Crotonase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	ClpP/crotonase	8067171	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8067171	3000033	SCOP2B (2022-06-29)
A	SCOP2 Family	Crotonase-like	8067170	4000036	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ClpP/crotonase	8067171	3000033	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)
C	HMG_CoA_synt_N	e2gtrC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: HMG_CoA_synt_N	ECOD (v294.1)
B	HMG_CoA_synt_N	e2gtrB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: HMG_CoA_synt_N	ECOD (v294.1)
A	SH3_1	e2gtrA1	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: SH3_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
C	1.10.12.10	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
B	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
B	1.10.12.10	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)
A	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
A	1.10.12.10	Mainly Alpha	Orthogonal Bundle	Lyase 2-enoyl-coa Hydratase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00378	Enoyl-CoA hydratase/isomerase (ECH_1)	Enoyl-CoA hydratase/isomerase	This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Chromodomain Y-like protein	transcription corepressor activity transcription regulator activity transcription coregulator activity enoyl-CoA hydratase activity (2E)-butenoyl-CoA hydratase activity hydro-lyase activity 3-hydroxyacyl-CoA dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity chromatin binding binding protein-macromolecule adaptor activity molecular adaptor activity transcription corepressor activity transcription regulator activity transcription coregulator activity enoyl-CoA hydratase activity (2E)-butenoyl-CoA hydratase activity hydro-lyase activity 3-hydroxyacyl-CoA dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity chromatin binding binding protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein binding	developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cell differentiation anatomical structure development developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction gamete generation male gamete generation cell differentiation anatomical structure development germ cell development cellular process regulation of cellular process peptidyl-lysine crotonylation regulation of protein modification process negative regulation of biological process regulation of primary metabolic process protein acylation negative regulation of protein modification process negative regulation of cellular process protein metabolic process protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process regulation of peptidyl-lysine crotonylation regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process negative regulation of peptidyl-lysine crotonylation macromolecule modification metabolic process macromolecule metabolic process regulation of metabolic process cellular component organization cellular component biogenesis cellular component assembly chromatin organization chromatin remodeling cellular component organization or biogenesis regulation of biosynthetic process random inactivation of X chromosome heterochromatin formation sex-chromosome dosage compensation epigenetic regulation of gene expression heterochromatin organization gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process dosage compensation by inactivation of X chromosome regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen chromosome cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR051053	Enoyl-CoA hydratase/isomerase and chromodomain-containing protein	Family
A, B, C	IPR000953	Chromo/chromo shadow domain	Domain
A, B, C	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B, C	IPR023780	Chromo domain	Domain
A, B, C	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B, C	IPR014748	Enoyl-CoA hydratase, C-terminal	Homologous Superfamily
A, B, C	IPR023779	Chromo domain, conserved site	Conserved Site
A, B, C	IPR001753	Enoyl-CoA hydratase/isomerase-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q9Y232	small cell lung carcinoma lung cancer malignant mesothelioma skin basal cell carcinoma malignant ependymoma medulloblastoma small cell carcinoma spina bifida malignant glioma psoriasis Small cell carcinoma of lung squamous cell carcinoma

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	histone acetyltransferase (crotonase type) M-CSA #344	A member of the crotonase superfamily. Histone acetyltransferase catalyses the acetylation of N-terminal lysine residues in histones, as part of the displacement of histones by transition proteins and protamines during vertebrate spermatogenesis.	Defined by 3 residues: LEU:A-66LEU:A-115ASP:A-146 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2.1 (UniProt) Search M-CSA Motif + EC 4.2.1

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.