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(-) Description

Title :  STRUCTURE OF THE RIBBON-HELIX-HELIX DOMAIN OF ESCHERICHIA COLI PUTA (PUTA52) COMPLEXED WITH OPERATOR DNA (O2)
 
Authors :  J. J. Tanner
Date :  18 Sep 07  (Deposition) - 29 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein-Dna Complex, Ribbon-Helix-Helix, Proline Utilization A, Puta, Dna-Binding, Fad, Flavoprotein, Multifunctional Enzyme, Nad, Oxidoreductase, Proline Metabolism, Repressor, Transcription, Transcription Regulation, Oxidoreductase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Zhou, J. D. Larson, C. A. Bottoms, E. C. Arturo, M. T. Henzl, J. L. Jenkins, J. C. Nix, D. F. Becker, J. J. Tanner
Structural Basis Of The Transcriptional Regulation Of The Proline Utilization Regulon By Multifunctional Puta.
J. Mol. Biol. V. 381 174 2008
PubMed-ID: 18586269  |  Reference-DOI: 10.1016/J.JMB.2008.05.084

(-) Compounds

Molecule 1 - BIFUNCTIONAL PROTEIN PUTA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKA8H
    Expression System StrainBL21 DE3 PLYSS
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-52
    GenePUTA, POAA
    Organism ScientificESCHERICHIA COLI
 
Molecule 2 - DNA (5'- D(*DTP*DT*DTP*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DTP *DCP*DAP*DAP*DA)-3')
    ChainsC
    EngineeredYES
    Other DetailsTHE NUCLEOTIDES 211-231 OF THE PUT CONTROL REGION IN E. COLI
    SyntheticYES
 
Molecule 3 - DNA (5'- D(*DTP*DTP*DTP*DGP*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DG P*DCP*DAP*DAP*DA)-3')
    ChainsD
    EngineeredYES
    Other DetailsCOMPLEMENT STRAND OF THE NUCLEOTIDES 211-231 OF THE PUT CONTROL REGION IN E. COLI
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 2RBF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RBF)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:44
 aligned with PUTA_ECOLI | P09546 from UniProtKB/Swiss-Prot  Length:1320

    Alignment length:44
                                    12        22        32        42    
            PUTA_ECOLI    3 TTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLEN 46
               SCOP domains d2rbfa_ A: Bifunctional protein putA         SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains -------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                  2rbf A  3 TTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLEN 46
                                    12        22        32        42    

Chain B from PDB  Type:PROTEIN  Length:45
 aligned with PUTA_ECOLI | P09546 from UniProtKB/Swiss-Prot  Length:1320

    Alignment length:45
                                    13        23        33        43     
            PUTA_ECOLI    4 TTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSD 48
               SCOP domains d2rbfb_ B: Bifunctional protein putA          SCOP domains
               CATH domains --------------------------------------------- CATH domains
               Pfam domains --------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  2rbf B  4 TTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSD 48
                                    13        23        33        43     

Chain C from PDB  Type:DNA  Length:19
                                                  
                  2rbf C  3 TGCGGTTGCACCTTTCAAA 21
                                    12         

Chain D from PDB  Type:DNA  Length:19
                                                  
                  2rbf D  1 TTTGAAAGGTGCAACCGCA 19
                                    10         

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PUTA_ECOLI | P09546)
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:0004029    aldehyde dehydrogenase (NAD) activity    Catalysis of the reaction: an aldehyde + NAD+ + H2O = an acid + NADH + H+.
    GO:0000986    bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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.
    GO:0001141    transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter.
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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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.
cellular component
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PUTA_ECOLI | P095461tiw 1tj0 1tj1 1tj2 2ay0 2fzm 2fzn 2gpe 3e2q 3e2r 3e2s 3itg 4jny 4jnz 4o8a

(-) Related Entries Specified in the PDB File

2ay0 THE LYS9MET MUTANT OF THIS PROTEIN WITHOUT BOUND DNA.
2gpe THE SAME PROTEIN WITHOUT BOUND DNA.