Annotations: 3CA8

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	Redoxin	e3ca8B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Redoxin	ECOD (v294.1)
A	DUF218	e3ca8A1	A: a/b three-layered sandwiches	X: HUP domain-like	H: YdcF	T: YdcF	F: DUF218	ECOD (v294.1)

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

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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.