5C8A | pdb_00005c8a

Crystal structure of a truncated form of Thermus thermophilus CarH bound to adenosylcobalamin (dark state)

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)
A	B12-binding_2	e5c8aA2	A: alpha arrays	X: Methionine synthase domain-like (From Topology)	H: Methionine synthase domain-like (From Topology)	T: Methionine synthase domain-like	F: B12-binding_2	ECOD (1.6)
A	B12-binding	e5c8aA1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
B	B12-binding_2	e5c8aB2	A: alpha arrays	X: Methionine synthase domain-like (From Topology)	H: Methionine synthase domain-like (From Topology)	T: Methionine synthase domain-like	F: B12-binding_2	ECOD (1.6)
B	B12-binding	e5c8aB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
C	B12-binding_2	e5c8aC2	A: alpha arrays	X: Methionine synthase domain-like (From Topology)	H: Methionine synthase domain-like (From Topology)	T: Methionine synthase domain-like	F: B12-binding_2	ECOD (1.6)
C	B12-binding	e5c8aC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
D	B12-binding_2	e5c8aD2	A: alpha arrays	X: Methionine synthase domain-like (From Topology)	H: Methionine synthase domain-like (From Topology)	T: Methionine synthase domain-like	F: B12-binding_2	ECOD (1.6)
D	B12-binding	e5c8aD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (utative)
A	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (utative)
B	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (utative)
B	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (utative)
C	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (utative)
C	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (utative)
D	1.10.1240.10	Mainly Alpha	Orthogonal Bundle	Methyltransferase, Methionine Synthase (B12-binding Domains)	Chain A, domain 1	CATH (utative)
D	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02607	B12 binding domain (B12-binding_2)	B12 binding domain	This B12 binding domain is found in methionine synthase EC:2.1.1.13 Swiss:Q99707, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of Pfam:PF02310. The structure of this domain is known [1], it is a 4 helix b ...	This B12 binding domain is found in methionine synthase EC:2.1.1.13 Swiss:Q99707, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of Pfam:PF02310. The structure of this domain is known [1], it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Light-dependent transcriptional regulator CarH	DNA binding binding nucleic acid binding vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding transcription regulator activity DNA-binding transcription factor activity cation binding ion binding metal ion binding identical protein binding DNA binding binding nucleic acid binding vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding transcription regulator activity DNA-binding transcription factor activity cation binding ion binding metal ion binding identical protein binding protein binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003759	Cobalamin (vitamin B12)-binding module, cap domain	Domain
A, B, C, D	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR047057	MerR transcriptional regulator	Family
A, B, C, D	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, B, C, D	IPR036594	Methionine synthase domain	Homologous Superfamily
A, B, C, D	IPR000551	MerR-type HTH domain	Domain

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.