3KJK | pdb_00003kjk

Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (monoclinic crystal form)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d3kjkl_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
K	d3kjkk_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
J	d3kjkj_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
I	d3kjki_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
H	d3kjkh_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
G	d3kjkg_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
F	d3kjkf_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
E	d3kjke_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
D	d3kjkd_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
C	d3kjkc_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
B	d3kjkb_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)
A	d3kjka_	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	YjgF-like	automated matches	automated matches	(Neisseria meningitidis serogroup B ) [TaxId: 491 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	YjgF-like	8059851	3001733	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	YjgF-like	8059851	3001733	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)
L	Ribonuc_L-PSP	e3kjkL1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
K	Ribonuc_L-PSP	e3kjkK1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
J	Ribonuc_L-PSP	e3kjkJ1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
I	Ribonuc_L-PSP	e3kjkI1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
H	Ribonuc_L-PSP	e3kjkH1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
G	Ribonuc_L-PSP	e3kjkG1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
F	Ribonuc_L-PSP	e3kjkF1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
E	Ribonuc_L-PSP	e3kjkE1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
D	Ribonuc_L-PSP	e3kjkD1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
C	Ribonuc_L-PSP	e3kjkC1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
B	Ribonuc_L-PSP	e3kjkB1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)
A	Ribonuc_L-PSP	e3kjkA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: YjgF-like (From Topology)	T: YjgF-like	F: Ribonuc_L-PSP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
K	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
J	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
I	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
H	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
G	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
F	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
E	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
C	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.30.1330.40	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF01042	Endoribonuclease L-PSP (Ribonuc_L-PSP)	Endoribonuclease L-PSP	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. Yjg ...	Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase [5]. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella [4].	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR019897	RidA, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR035959	RutC-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR035709	RutC family, YoaB-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006175	YjgF/YER057c/UK114 family	Family

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.