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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI PUTA PROLINE DEHYDROGENASE DOMAIN (RESIDUES 86-669) COMPLEXED WITH ACETATE
 
Authors :  J. J. Tanner, M. Zhang, T. A. White, J. P. Schuermann, B. A. Baban, D. F. Be
Date :  03 Jun 04  (Deposition) - 26 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Beta/Alpha Barrel, Flavoenzyme, Fad, Proline Catabolism, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Zhang, T. A. White, J. P. Schuermann, B. A. Baban, D. F. Becker, J. J. Tanner
Structures Of The Escherichia Coli Puta Proline Dehydrogenase Domain In Complex With Competitive Inhibitors
Biochemistry V. 43 12539 2004
PubMed-ID: 15449943  |  Reference-DOI: 10.1021/BI048737E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIFUNCTIONAL PUTA PROTEIN
    ChainsA
    EC Number1.5.99.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-23B
    Expression System StrainBL21 DE3 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentE. COLI PUTA PROLINE DEHYDROGENASE DOMAIN (RESIDUES 86- 669)
    GenePUTA, POAA, B1014
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:329 , ALA A:436 , TYR A:552 , ARG A:555 , ARG A:556 , FAD A:2001BINDING SITE FOR RESIDUE ACT A 2002
2AC2SOFTWAREASP A:370 , ALA A:371 , VAL A:402 , GLN A:404 , TYR A:406 , ARG A:431 , VAL A:433 , LYS A:434 , GLY A:435 , ALA A:436 , TYR A:437 , TRP A:438 , TYR A:456 , THR A:457 , ARG A:458 , LYS A:459 , THR A:462 , ALA A:485 , THR A:486 , HIS A:487 , ASN A:488 , GLN A:511 , CYS A:512 , LEU A:513 , TYR A:540 , ARG A:556 , GLU A:559 , SER A:565 , PHE A:566 , ACT A:2002 , HOH A:2029 , HOH A:2045 , HOH A:2055 , HOH A:2115BINDING SITE FOR RESIDUE FAD A 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TJ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TJ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TJ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TJ2)

(-) Exons   (0, 0)

(no "Exon" information available for 1TJ2)

(-) Sequences/Alignments

Asymmetric Unit
   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:450
 aligned with PUTA_ECOLI | P09546 from UniProtKB/Swiss-Prot  Length:1320

    Alignment length:523
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607   
           PUTA_ECOLI    88 QSVSRAAITAAYRRPETEAVSMLLEQARLPQPVAEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSGEPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDLATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLIYPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRD 610
               SCOP domains -d1tj2a1 A:89-261 N-terminal domain of bifunctional PutA pro              tein                                                                                                d1tj2a2 A:262-610 Proline dehydrohenase domain of bifunctional PutA protein                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1tj2A01 A:88-146,A:244-610                                 -------------------------------------------------------------------------------------------------1tj2A01 A:88-146,A:244-610  [code=3.20.20.220, no name defined]                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------Pro_dh-1tj2A01 A:244-574                                                                                                                                                                                                                                                                                                                   ------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..........--------------hhhhhhhhhhhhh..hhhhhhhh-----------------------------------------------------------hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeehhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh....hhhhheeeee...hhhhhh....hhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhh.hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tj2 A  88 QSVSRAAITAAYRRPETEAVSMLLEQARLPQPVAEQAHKLAYQLADKLRNQKNASGRAGM--------------GVALMCLAEALLRIPDKATRDAL-----------------------------------------------------------IRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDLATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLIYPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRD 610
                                    97       107       117       127       137       147         -    |  167       177      |  -         -         -         -         -         -      |247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607   
                                                                                     147            162                   184                                                         244                                                                                                                                                                                                                                                                                                                                                                              

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 2ay0 2fzm 2fzn 2gpe 2rbf 3e2q 3e2r 3e2s 3itg 4jny 4jnz 4o8a

(-) Related Entries Specified in the PDB File

1k87 RELATED E. COLI PUTA PROLINE DEHYDROGENASE CONSTRUCT COMPLEXED WITH L-LACTATE
1tiw THE SAME PROTEIN COMPLEXED WITH L-TETRAHYDRO-2-FUROIC ACID; CRYSTAL GROWN IN PEG 3350
1tj0 THE SAME PROTEIN COMPLEXED WITH L-LACTATE; CRYSTAL GROWN IN PEG 3350 AND 10 MM L-LACTATE
1tj1 THE SAME PROTEIN COMPLEXED WITH L-LACTATE; CRYSTAL GROWN IN PEG3000