2AY0 | pdb_00002ay0

Structure of the Lys9Met mutant of the E. coli Proline Utilization A (PutA) DNA-binding domain.

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)
A	d2ay0a1	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	Bifunctional protein putA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2ay0b_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	Bifunctional protein putA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2ay0c_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	Bifunctional protein putA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2ay0d_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	Bifunctional protein putA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2ay0e_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	Bifunctional protein putA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2ay0f_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	Bifunctional protein putA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PutA pre-N-terminal region-like	8021124	4001365	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribbon-helix-helix	8033504	3000295	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribbon-helix-helix	8033504	3000295	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribbon-helix-helix	8033504	3000295	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribbon-helix-helix	8033504	3000295	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribbon-helix-helix	8033504	3000295	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribbon-helix-helix	8033504	3000295	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	putA_1st	e2ay0A1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: putA_1st	ECOD (1.6)
B	putA_1st	e2ay0B1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: putA_1st	ECOD (1.6)
C	putA_1st	e2ay0C1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: putA_1st	ECOD (1.6)
D	putA_1st	e2ay0D1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: putA_1st	ECOD (1.6)
E	putA_1st	e2ay0E1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: putA_1st	ECOD (1.6)
F	putA_1st	e2ay0F1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: putA_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
B	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
C	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
D	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
E	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
F	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	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	PF21775	PutA, RHH domain (PutA_1st)	PutA, RHH domain	This domain is found in the Bifunctional protein PutA from Escherichia coli and similar sequences mainly found in proteobacteria. PutA is both a bifunctional proline catabolic enzyme that oxidises proline to glutamate for use as a carbon and nitrogen ...	This domain is found in the Bifunctional protein PutA from Escherichia coli and similar sequences mainly found in proteobacteria. PutA is both a bifunctional proline catabolic enzyme that oxidises proline to glutamate for use as a carbon and nitrogen source and an autogenous transcriptional repressor of the put operon. This entry represents the N-terminal ribbon-helix-helix (RHH) domain, which consists of a beta-strand and two alpha-helices. This domain has a Lys at the end of the beta-strand that interacts directly with DNA bases through the major groove, contributing to transcriptional regulation [1,3].	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	Bifunctional putA protein	flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding sequence-specific DNA binding DNA binding nucleic acid binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding sequence-specific DNA binding DNA binding nucleic acid binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 1-pyrroline-5-carboxylate dehydrogenase activity oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors proline dehydrogenase activity oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor	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 glutamine family amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process proline metabolic process small molecule metabolic process proline biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process catabolic process glutamine family amino acid catabolic process organic acid catabolic process proline catabolic process carboxylic acid catabolic process glutamate metabolic process amino acid catabolic process proline catabolic process to glutamate dicarboxylic acid metabolic process L-amino acid catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process small molecule catabolic process response to oxidative stress response to stimulus response to stress	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR002872	Proline dehydrogenase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR015590	Aldehyde dehydrogenase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR048798	PutA, RHH domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR016161	Aldehyde/histidinol dehydrogenase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029041	FAD-linked oxidoreductase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR025703	Bifunctional protein PutA	Family
A, B, C, D, E A, B, C, D, E, F	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR029510	Aldehyde dehydrogenase, glutamic acid active site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR024089	Proline dehydrogenase PutA, domain I/II	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR016160	Aldehyde dehydrogenase, cysteine active site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR024082	Proline dehydrogenase PutA, domain II	Domain
A, B, C, D, E A, B, C, D, E, F	IPR016162	Aldehyde dehydrogenase, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR041349	Proline utilization A proline dehydrogenase N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050485	Proline metabolism enzyme	Family
A, B, C, D, E A, B, C, D, E, F	IPR024090	Proline dehydrogenase PutA, domain I	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR016163	Aldehyde dehydrogenase, C-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR005933	Bifunctional protein PutA, C-terminal 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.