1L1D

Crystal structure of the C-terminal methionine sulfoxide reductase domain (MsrB) of N. gonorrhoeae pilB

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1l1da_	All beta proteins	Mss4-like	Mss4-like	SelR domain	C-terminal MsrB domain of peptide methionine sulfoxide reductase PilB	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)
B	d1l1db_	All beta proteins	Mss4-like	Mss4-like	SelR domain	C-terminal MsrB domain of peptide methionine sulfoxide reductase PilB	(Neisseria gonorrhoeae ) [TaxId: 485 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SelR domain	8028574	4002166	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Mss4-like	8040953	3001994	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Mss4-like	8040953	3001994	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SelR	e1l1dA1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: SelR	ECOD (1.6)
B	SelR	e1l1dB1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: SelR	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)
B	2.170.150.20	Mainly Beta	Beta Complex	Metal Binding Protein, Guanine Nucleotide Exchange Factor	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01641	SelR domain (SelR)	SelR domain	Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and h ...	Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterised with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidised methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain Pfam:PF01625. The domain has two conserved cysteines and histidines. The domain binds both selenium and zinc [2]. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family [1]. This family has methionine-R-sulfoxide reductase activity [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	peptide methionine sulfoxide reductase	oxidoreductase activity, acting on a sulfur group of donors oxidoreductase activity oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor catalytic activity peptide-methionine (R)-S-oxide reductase activity peptide-methionine (S)-S-oxide reductase activity L-methionine-(S)-S-oxide reductase activity L-methionine:thioredoxin-disulfide S-oxidoreductase activity	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002569	Peptide methionine sulphoxide reductase MsrA domain	Domain
A, B	IPR036509	Peptide methionine sulphoxide reductase MsrA superfamily	Homologous Superfamily
A, B	IPR013766	Thioredoxin domain	Domain
A, B	IPR011057	Mss4-like superfamily	Homologous Superfamily
A, B	IPR050162	Methionine Sulfoxide Reductase A	Family
A, B	IPR013740	Redoxin	Domain
A, B	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, B	IPR002579	Peptide methionine sulphoxide reductase MrsB domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	protein-methionine-S-oxide reductase (MsrB) M-CSA #715	The oxidation of methionine residues to methionine sulfoxide is implicated in ageing processes; the reduction of methionine sulfoxide protein residues is similarly implicated in antioxidant repair activity, but also the virulence of pathogenic organisms, such as Neisseria gonorrhoeae which secretes pilB. The modular pilB contains three domains; one is a methionine sulfoxide reductase (MsrA) which reduces S-methionine sulfoxide (S-chiral at sulphur), and another an MsrB (this entry) which reduces R-methionine sulfoxide. The two domains have no sequence homology but use the same mechanism - an example of the fusion of two convergently evolved enzymes.	Defined by 6 residues: CYS:B-70 [auth B-440]HIS:B-107 [auth B-477]HIS:B-110 [auth B-480]ASP:B-114 [auth B-484]ARG:B-123 [auth B-493]CYS:B-125 [auth B-495] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.8.4.13 (PDB Primary Data) Search M-CSA Motif + EC 1.8.4.13 EC: 1.8.4.14 (PDB Primary Data) Search M-CSA Motif + EC 1.8.4.14 EC: 1.8.4.11 (UniProt) Search M-CSA Motif + EC 1.8.4.11 EC: 1.8.4.12 (UniProt) Search M-CSA Motif + EC 1.8.4.12

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.