2JH3 | pdb_00002jh3

The crystal structure of DR2241 from Deinococcus radiodurans at 1.9 A resolution reveals a multi-domain protein with structural similarity to chelatases but also with two additional novel domains

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)
D	EUF08006	e2jh3D3	A: alpha arrays	X: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	H: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	T: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein	F: EUF08006	ECOD (1.6)
D	EUF08445	e2jh3D2	A: a+b two layers	X: Middle domain of ribosomal protein S2-related protein (From Topology)	H: Middle domain of ribosomal protein S2-related protein (From Topology)	T: Middle domain of ribosomal protein S2-related protein	F: EUF08445	ECOD (1.6)
D	CbiX	e2jh3D1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: CbiX	ECOD (1.6)
C	EUF08006	e2jh3C3	A: alpha arrays	X: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	H: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	T: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein	F: EUF08006	ECOD (1.6)
C	EUF08445	e2jh3C2	A: a+b two layers	X: Middle domain of ribosomal protein S2-related protein (From Topology)	H: Middle domain of ribosomal protein S2-related protein (From Topology)	T: Middle domain of ribosomal protein S2-related protein	F: EUF08445	ECOD (1.6)
C	CbiX	e2jh3C1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: CbiX	ECOD (1.6)
B	EUF08006	e2jh3B3	A: alpha arrays	X: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	H: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	T: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein	F: EUF08006	ECOD (1.6)
B	EUF08445	e2jh3B2	A: a+b two layers	X: Middle domain of ribosomal protein S2-related protein (From Topology)	H: Middle domain of ribosomal protein S2-related protein (From Topology)	T: Middle domain of ribosomal protein S2-related protein	F: EUF08445	ECOD (1.6)
B	CbiX	e2jh3B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: CbiX	ECOD (1.6)
A	EUF08006	e2jh3A3	A: alpha arrays	X: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	H: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein (From Topology)	T: C-terminal 4Fe-4S binding domain of ribosomal protein S2-related protein	F: EUF08006	ECOD (1.6)
A	EUF08445	e2jh3A2	A: a+b two layers	X: Middle domain of ribosomal protein S2-related protein (From Topology)	H: Middle domain of ribosomal protein S2-related protein (From Topology)	T: Middle domain of ribosomal protein S2-related protein	F: EUF08445	ECOD (1.6)
A	CbiX	e2jh3A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Chelatase-like	F: CbiX	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.1400	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.30.1360.190	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
D	3.30.70.2320	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	3.40.50.1400	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.30.1360.190	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
C	3.30.70.2320	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.40.50.1400	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.1360.190	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
B	3.30.70.2320	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.40.50.1400	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.1360.190	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	3.30.70.2320	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF18069	DR2241 stabilising domain (DR2241)	DR2241 stabilising domain	This is the middle domain found in DR2241, a multi-domain protein with an N-terminal cobalamin (vitamin B12) chelatase domain. DR2241 is found in D. radiodurans. The middle domain has four alpha-helices (alpha7-alpha10) in contact with the N-terminal ...	This is the middle domain found in DR2241, a multi-domain protein with an N-terminal cobalamin (vitamin B12) chelatase domain. DR2241 is found in D. radiodurans. The middle domain has four alpha-helices (alpha7-alpha10) in contact with the N-terminal domains and C-terminal domain and five anti-parallel beta-strands with strand order 12354 at the outer side of one monomer. The middle domain, as well as the C-terminal domain, are heavily involved in the tetramer stabilisation [1].	Domain
A, B, C, D	PF01903	CbiX (CbiX)	CbiX	The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine-rich region at their C-terminus, which suggests that it might be involved in ...	The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine-rich region at their C-terminus, which suggests that it might be involved in metal chelation [1].	Domain
A, B, C, D	PF18009	4Fe-4S iron-sulfur cluster binding domain (Fer4_23)	4Fe-4S iron-sulfur cluster binding domain	This is the C-terminal domain found in Deinococcus radiodurans protein DR2241 (a Ribosomal protein S2-related protein). This domain has been shown to harbour the sequence motifs CxxC and CxxxC which bind a [4Fe-4S] iron-sulphur cluster. Together with ...	This is the C-terminal domain found in Deinococcus radiodurans protein DR2241 (a Ribosomal protein S2-related protein). This domain has been shown to harbour the sequence motifs CxxC and CxxxC which bind a [4Fe-4S] iron-sulphur cluster. Together with the preceding domain, it is heavily involved in the tetramer formation [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RIBOSOMAL PROTEIN S2-RELATED PROTEIN	lyase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012374	Co/Fe-chelatase, CbiX-related	Family
A, B, C, D	IPR050963	Sirohydrochlorin Cobaltochelatase/CbiX	Family
A, B, C, D	IPR002762	Sirohydrochlorin cobaltochelatase CbiX-like	Family
A, B, C, D	IPR041346	DR2241, 4Fe-4S iron-sulfur cluster binding domain	Domain
A, B, C, D	IPR041181	DR2241 stabilising 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.