2P5V | pdb_00002p5v

Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product 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)
H	d2p5vh1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
H	d2p5vh2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
G	d2p5vg1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
G	d2p5vg2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
F	d2p5vf1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
F	d2p5vf2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
E	d2p5ve1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
E	d2p5ve2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
D	d2p5vd1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
D	d2p5vd2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
C	d2p5vc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
C	d2p5vc2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
B	d2p5vb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
B	d2p5vb2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
A	d2p5va1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)
A	d2p5va2	Alpha and beta proteins (a+b)	Ferredoxin-like	Dimeric alpha+beta barrel	automated matches	automated matches	(Neisseria meningitidis MC58 ) [TaxId: 122586 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	HTHP	e2p5vH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
G	HTHP	e2p5vG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
F	HTHP	e2p5vF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
E	HTHP	e2p5vE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
D	HTHP	e2p5vD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
C	HTHP	e2p5vC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
B	HTHP	e2p5vB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: HTHP	ECOD (v294.1)
A	Cystatin	e2p5vA1	A: a/b three-layered sandwiches	X: Profilin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Cystatin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
H	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	CATH (4.3.0)
G	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
G	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	CATH (4.3.0)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
F	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	CATH (4.3.0)
E	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	3.30.70.920	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain	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	PF01037	Lrp/AsnC ligand binding domain (AsnC_trans_reg)	Lrp/AsnC ligand binding domain	The l-leucine-responsive regulatory protein (Lrp/AsnC) family is a family of similar bacterial transcription regulatory proteins. The family is named after two E. coli proteins involved in regulating amino acid metabolism. This entry corresponds to t ...	The l-leucine-responsive regulatory protein (Lrp/AsnC) family is a family of similar bacterial transcription regulatory proteins. The family is named after two E. coli proteins involved in regulating amino acid metabolism. This entry corresponds to the usually C-terminal regulatory ligand binding domain. Structurally this domain has a dimeric alpha/beta barrel fold [2]. This domain binds almost exclusively amino acids but also 4-hydroxyphenylpyruvate and kynurenine (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF13412	Winged helix-turn-helix DNA-binding (HTH_24)	Winged helix-turn-helix DNA-binding		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Transcriptional regulator, LRP/AsnC family	sequence-specific DNA binding DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	response to acid chemical response to stimulus response to chemical response to amino acid regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process response to acid chemical response to stimulus response to chemical response to amino acid regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011991	ArsR-like helix-turn-helix domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019887	Transcription regulator AsnC/Lrp, ligand binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019888	Transcription regulator AsnC-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR019885	Transcription regulator HTH, AsnC-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000485	AsnC-type HTH domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011008	Dimeric alpha-beta barrel	Homologous Superfamily

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.