6PEU | pdb_00006peu

Structure of YcaO enzyme from Methanocaldococcus jannaschii in complex with peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YcaO_2nd	e6peuA3	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_2nd	ECOD (1.6)
A	YcaO_1st	e6peuA1	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_1st	ECOD (1.6)
A	UNK_F_TYPE	e6peuA2	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)
B	YcaO_2nd	e6peuB3	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_2nd	ECOD (1.6)
B	YcaO_1st	e6peuB1	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_1st	ECOD (1.6)
B	UNK_F_TYPE	e6peuB2	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)
C	YcaO_2nd	e6peuC1	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_2nd	ECOD (1.6)
C	YcaO_1st	e6peuC2	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_1st	ECOD (1.6)
C	UNK_F_TYPE	e6peuC3	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)
D	YcaO_2nd	e6peuD1	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_2nd	ECOD (1.6)
D	YcaO_1st	e6peuD3	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: YcaO_1st	ECOD (1.6)
D	UNK_F_TYPE	e6peuD2	A: a+b two layers	X: dsRBD-like	H: Heterocyclase TruD C-terminal domain (From Topology)	T: Heterocyclase TruD C-terminal domain	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02624	YcaO cyclodehydratase, ATP-ad Mg2+-binding (YcaO)	YcaO cyclodehydratase, ATP-ad Mg2+-binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Uncharacterized protein MJ1094	-	-	-
E [auth M], F [auth N], G [auth P], H [auth Q]	GLY-ARG-LEU-GLY-PHE-TYR-GLY-TYR-ASP-LEU-GLN-ASP	coenzyme-B sulfoethylthiotransferase activity alkylthioltransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process alkane metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003776	YcaO-like domain	Domain
A, B, C, D	IPR017667	YcaO-related McrA-glycine thioamidation protein	Family
E [auth M], F [auth N], G [auth P], H [auth Q]	IPR009047	Methyl-coenzyme M reductase, alpha subunit, C-terminal	Domain
E [auth M], F [auth N], G [auth P], H [auth Q]	IPR009024	Methyl-coenzyme M reductase, ferredoxin-like fold	Homologous Superfamily
E [auth M], F [auth N], G [auth P], H [auth Q]	IPR003183	Methyl-coenzyme M reductase, alpha subunit, N-terminal	Domain
E [auth M], F [auth N], G [auth P], H [auth Q]	IPR008924	Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal	Homologous Superfamily
E [auth M], F [auth N], G [auth P], H [auth Q]	IPR016212	Methyl coenzyme M reductase, alpha subunit	Family
E [auth M], F [auth N], G [auth P], H [auth Q]	IPR015823	Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2	Homologous Superfamily
E [auth M], F [auth N], G [auth P], H [auth Q]	IPR015811	Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1	Homologous Superfamily

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.