2JXI

Solution structure of the DNA-binding domain of Pseudomonas putida Proline utilization A (putA) bound to GTTGCA DNA sequence

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	d2jxia_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B	d2jxib_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	PutA pre-N-terminal region-like	automated matches	(Pseudomonas putida ) [TaxId: 303 ],	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	8074027	4001365	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribbon-helix-helix	8074028	3000295	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribbon-helix-helix	8074028	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	PF21775	e2jxiA1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF21775	ECOD (1.6)
B	PF21775	e2jxiB1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF21775	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Proline dehydrogenase	DNA binding binding organic cyclic compound binding nucleic acid binding 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 transcription regulator activity DNA-binding transcription factor activity	catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process proline catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process cellular catabolic process proline metabolic process organic substance metabolic process carboxylic acid catabolic process glutamate metabolic process catabolic process oxoacid metabolic process glutamine family amino acid catabolic process amino acid metabolic process organic acid metabolic process organic acid catabolic process proline catabolic process alpha-amino acid metabolic process glutamine family amino acid metabolic process cellular catabolic process proline metabolic process organic substance metabolic process carboxylic acid catabolic process glutamate metabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process proline catabolic process to glutamate organonitrogen compound metabolic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process glutamine family amino acid biosynthetic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process organic substance biosynthetic process proline biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process alpha-amino acid biosynthetic process	-
C	DNA (5'-D(DGPDCPDGPDGPDTPDTPDGPDCPDAPDCPDCPDTPDTPDT)-3')	-	-	-
D	DNA (5'-D(DAPDAPDAPDGPDGPDTPDGPDCPDAPDAPDCPDCPDGPDC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002872	Proline dehydrogenase domain	Domain
A, B	IPR015590	Aldehyde dehydrogenase domain	Domain
A, B	IPR048798	PutA, RHH domain	Domain
A, B	IPR016161	Aldehyde/histidinol dehydrogenase	Homologous Superfamily
A, B	IPR029041	FAD-linked oxidoreductase-like	Homologous Superfamily
A, B	IPR016162	Aldehyde dehydrogenase, N-terminal	Homologous Superfamily
A, B	IPR041349	Proline utilization A proline dehydrogenase N-terminal domain	Domain
A, B	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A, B	IPR025703	Bifunctional protein PutA	Family
A, B	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A, B	IPR024090	Proline dehydrogenase PutA, domain I	Homologous Superfamily
A, B	IPR024089	Proline dehydrogenase PutA, domain I/II	Homologous Superfamily
A, B	IPR016163	Aldehyde dehydrogenase, C-terminal	Homologous Superfamily
A, B	IPR016160	Aldehyde dehydrogenase, cysteine active site	Conserved Site
A, B	IPR005933	Bifunctional protein PutA, C-terminal domain	Domain
A, B	IPR024082	Proline dehydrogenase PutA, domain II	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 R01GM133198.