2JXI - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE DNA-BINDING DOMAIN OF PSEUDOMONAS PUTIDA PROLINE UTILIZATION A (PUTA) BOUND TO GTTGCA DNA SEQUENCE

Authors :   S. Halouska, Y. Zhou, D. Becker, R. Powers

Date :   19 Nov 07 (Deposition) - 21 Oct 08 (Release) - 27 May 15 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C,D
NMR Structure *: A,B,C,D  (1x)

Keywords :   Puta, Proline, Utilization, Dna, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Halouska, Y. Zhou, D. F. Becker, R. Powers
Solution Structure Of The Pseudomonas Putida Protein Ppputa45 And Its Dna Complex
Proteins V. 75 12 2008
PubMed-ID: 18767154 | Reference-DOI: 10.1002/PROT.22217

Molecule 1 - PROLINE DEHYDROGENASE
	Chains	:	A, B
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

*Molecule 2 - DNA (5'- D(DGPDCPDGPDGPDTPDTPDGPDCPDAPDCPDCPDTPDTPDT)-3')*
	Chains	:	C
	Engineered	:	YES
	Organism Taxid	:	32630
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(DAPDAPDAPDGPDGPDTPDGPDCPDAPDAPDCPDCPDGPDC)-3')*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
NMR Structure	:	A	B	C	D
NMR Structure * (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2JXI)

(no "Site" information available for 2JXI)

(no "SS Bond" information available for 2JXI)

(no "Cis Peptide Bond" information available for 2JXI)

(no "SAP(SNP)/Variant" information available for 2JXI)

(no "PROSITE Motif" information available for 2JXI)

(no "Exon" information available for 2JXI)

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:45
 aligned with Q88D80_PSEPK | Q88D80 from UniProtKB/TrEMBL  Length:1317

    Alignment length:45
                                    10        20        30        40     
          Q88D80_PSEPK    1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 45
               SCOP domains d2jxia_ A: automated matches                  SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  2jxi A  1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 45
                                    10        20        30        40

Chain A from PDB  Type:PROTEIN  Length:45
 aligned with Q9R9T7_PSEPU | Q9R9T7 from UniProtKB/TrEMBL  Length:1315

    Alignment length:45
                                    10        20        30        40     
          Q9R9T7_PSEPU    1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 45
               SCOP domains d2jxia_ A: automated matches                  SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ....ee...eehhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  2jxi A  1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 45
                                    10        20        30        40

Chain B from PDB  Type:PROTEIN  Length:45
 aligned with Q88D80_PSEPK | Q88D80 from UniProtKB/TrEMBL  Length:1317

    Alignment length:45
                                    10        20        30        40     
          Q88D80_PSEPK    1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 45
               SCOP domains d2jxib_ B: automated matches                  SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ..ee...ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  2jxi B 46 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 90
                                    55        65        75        85

Chain B from PDB  Type:PROTEIN  Length:45
 aligned with Q9R9T7_PSEPU | Q9R9T7 from UniProtKB/TrEMBL  Length:1315

    Alignment length:45
                                    10        20        30        40     
          Q9R9T7_PSEPU    1 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 45
               SCOP domains d2jxib_ B: automated matches                  SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author ..ee...ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  2jxi B 46 MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLE 90
                                    55        65        75        85

Chain C from PDB  Type:DNA  Length:14
                                             
                  2jxi C  1 GCGGTTGCACCTTT 14
                                    10

Chain D from PDB  Type:DNA  Length:14
                                             
                  2jxi D 15 AAAGGTGCAACCGC 28
                                    24

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Ribbon-helix-helix (65)

Superfamily: Ribbon-helix-helix (65)

Family: PutA pre-N-terminal region-like (6)

Protein domain: automated matches (4)

Pseudomonas putida [TaxId: 303] (3)

1a	d2jxia_	A:
1b	d2jxib_	B:

(no "CATH Domain" information available for 2JXI)

(no "Pfam Domain" information available for 2JXI)

NMR Structure(hide GO term definitions)

Chain A,B (Q9R9T7_PSEPU | Q9R9T7)

molecular function
	GO:0003842	1-pyrroline-5-carboxylate dehydrogenase activity	Catalysis of the reaction: 1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH + H(+).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
	GO:0004657	proline dehydrogenase activity	Catalysis of the reaction: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006561	proline biosynthetic process	The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
	GO:0010133	proline catabolic process to glutamate	The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including glutamate.
	GO:0006560	proline metabolic process	The chemical reactions and pathways involving proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Chain A,B (Q88D80_PSEPK | Q88D80)

molecular function
	GO:0003842	1-pyrroline-5-carboxylate dehydrogenase activity	Catalysis of the reaction: 1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH + H(+).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
	GO:0004657	proline dehydrogenase activity	Catalysis of the reaction: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006561	proline biosynthetic process	The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
	GO:0010133	proline catabolic process to glutamate	The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including glutamate.
	GO:0006560	proline metabolic process	The chemical reactions and pathways involving proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

NMR Structure
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jxi)

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	2jxi
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	Q88D80_PSEPK \| Q88D80
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	Q9R9T7_PSEPU \| Q9R9T7
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UniProtKB/TrEMBL
	Q9R9T7_PSEPU \| Q9R9T7	:	2jxg 2jxh

Description

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