3LGH | pdb_00003lgh

Crystal structure of NikR from Helicobacter pylori with variable Ni site coordination

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3lghd_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
C	d3lghc_	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
B	d3lghb1	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
B	d3lghb2	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
A	d3lgha1	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)
A	d3lgha2	Alpha and beta proteins (a+b)	Ferredoxin-like	ACT-like	automated matches	automated matches	Campylobacter pylori (Helicobacter pylori 26695 ) [TaxId: 85962 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
C	SCOP2 Family	Nickel responsive regulator NikR, C-terminal domain	8074827	4001483	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	ACT-like	8074828	3000006	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ACT-like	8074828	3000006	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ACT-like	8074828	3000006	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)
D		e3lghD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (v294.1)
C		e3lghC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (v294.1)
B		e3lghB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F:	ECOD (v294.1)
A	NikR_C	e3lghA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: NikR_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
C	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
B	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
B	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)
A	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
A	3.30.70.1150	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	ACT-like. Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08753	NikR C terminal nickel binding domain (NikR_C)	NikR C terminal nickel binding domain	NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains fou ...	NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains four nickel binding sites at the tetramer interface [1].	Domain
A, B, C, D	PF01402	Ribbon-helix-helix protein, copG family (RHH_1)	Ribbon-helix-helix protein, copG family	The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement [2]. The helix-turn-helix-like structure is involved in dimerisation and not DNA b ...	The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement [2]. The helix-turn-helix-like structure is involved in dimerisation and not DNA binding as might have been expected [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	nickel-responsive regulator	DNA binding binding nucleic acid binding cation binding transition metal ion binding ion binding nickel cation binding metal ion binding small molecule binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding DNA binding binding nucleic acid binding cation binding transition metal ion binding ion binding nickel cation binding metal ion binding small molecule binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding identical protein binding protein binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to stimulus response to metal ion response to chemical response to nickel cation	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR022988	Nickel-responsive transcriptional regulator NikR	Family
A, B, C, D	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A, B, C, D	IPR027271	Acetolactate synthase/Transcription factor NikR, C-terminal	Homologous Superfamily
A, B, C, D	IPR045865	ACT-like domain	Homologous Superfamily
A, B, C, D	IPR014864	Transcription factor, NikR, nickel binding C-terminal	Domain
A, B, C, D	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A, B, C, D	IPR002145	Ribbon-helix-helix protein, CopG	Domain
A, B, C, D	IPR050192	Nickel-responsive transcriptional regulator	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.