3CA8 | pdb_00003ca8

Crystal structure of Escherichia coli YdcF, an S-adenosyl-L-methionine utilizing enzyme

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	DUF218	e3ca8B1	A: a/b three-layered sandwiches	X: HUP domain-like	H: YdcF (From Topology)	T: YdcF	F: DUF218	ECOD (1.6)
A	DUF218	e3ca8A1	A: a/b three-layered sandwiches	X: HUP domain-like	H: YdcF (From Topology)	T: YdcF	F: DUF218	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.3620.10	Mainly Alpha	Orthogonal Bundle	YdcF fold	YdcF like domain	CATH (4.3.0)
B	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
A	1.10.3620.10	Mainly Alpha	Orthogonal Bundle	YdcF fold	YdcF like domain	CATH (4.3.0)
A	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02698	DUF218 domain (DUF218)	DUF218 domain	This domain contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The entry includes SanA Swiss:P33017 and Sfix (Swiss:O33790) from Salmonella typhimurium which are involved in Vancom ...	This domain contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The entry includes SanA Swiss:P33017 and Sfix (Swiss:O33790) from Salmonella typhimurium which are involved in Vancomycin resistance [1]. These proteins may be involved in murein synthesis [2]. This domain is found in Escherichia coli YdcF, which has been shown to bind S-adenosyl-L-methionine (AdoMet), but whose biochemical function has not been identified [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protein ydcF	-	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR051599	Cell Envelope Integrity and Synthesis Associated Protein	Family
A, B	IPR003848	Domain of unknown function DUF218	Domain
A, B	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	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.