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(-) Description

Title :  CRYSTAL STRUCTURE OF DELTA1-PIPERIDEINE-2-CARBOXYLATE REDUCTASE FROM PSEUDOMONAS SYRINGAE PVAR.TOMATO
 
Authors :  M. Goto, H. Muramatsu, H. Mihara, T. Kurihara, N. Esaki, R. Omi, I. Miyahara, K. Hirotsu
Date :  24 Nov 04  (Deposition) - 04 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nadph Dependent Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Goto, H. Muramatsu, H. Mihara, T. Kurihara, N. Esaki, R. Omi, I. Miyahara, K. Hirotsu
Crystal Structures Of Delta1-Piperideine-2-Carboxylate/Delta1-Pyrroline- 2-Carboxylate Reductase Belonging To A New Family Of Nad(P)H-Dependent Oxidoreductases: Conformational Change, Substrate Recognition, And Stereochemistry Of The Reaction
J. Biol. Chem. V. 280 40875 2005
PubMed-ID: 16192274  |  Reference-DOI: 10.1074/JBC.M507399200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UREIDOGLYCOLATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.154
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DPKA
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. TOMATO
    Organism Taxid: 323
    Synonym: DELTA(1)-PIPERIDEINE-2-CARBOXYLATE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WTJ)

(-) Sites  (0, 0)

(no "Site" information available for 1WTJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WTJ)

(-) Sequences/Alignments

Asymmetric/Biological 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:332
 aligned with PY2CR_PSEUB | Q4U331 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:332
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  
          PY2CR_PSEUB    10 TQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVRQLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQELA 341
               SCOP domains d1wtja_ A: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee....hhhhhhhhhhh..eeeee.....................eeeeeee..eeeeeeee.....hhhhhhhhhhh........ee.....ee.hhhhhhh..ee....hhhhhhhhhhhhhhhh......................eeeeeeeee........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wtj A  10 TQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVRQLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQELA 341
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339  


Chain B from PDB  Type:PROTEIN  Length:337
 aligned with PY2CR_PSEUB | Q4U331 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:337
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       
          PY2CR_PSEUB     7 DQPTQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVRQLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQELAGH 343
               SCOP domains d1wtjb_ B: automated matches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.........eeeeee..eeeee....hhhhhhhhhhhhhhhhhhhhheeeeeeeeee....hhhhhhhhhhh..eeeeee....................eeeeeee..eeeeeeee.....hhhhhhhhhhh........ee.....ee.hhhhhhh..ee....hhhhhhhhhhhhhhhh......................eeeeeeeee........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheeeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wtj B   7 DQPTQTVSYPQLIDLLRRIFVVHGTSPEVADVLAENCASAQRDGSHSHGIFRIPGYLSSLASGWVDGKAVPVVEDVGAAFVRVDACNGFAQPALAAARSLLIDKARSAGVAILAIRGSHHFAALWPDVEPFAEQGLVALSMVNSMTCVVPHGARQPLFGTNPIAFGAPRAGGEPIVFDLATSAIAHGDVQIAAREGRLLPAGMGVDRDGLPTQEPRAILDGGALLPFGGHKGSALSMMVELLAAGLTGGNFSFEFDWSKHPGAQTPWTGQLLIVIDPDKGAGQHFAQRSEELVRQLHGVGQERLPGDRRYLERARSMAHGIVIAQADLERLQELAGH 343
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WTJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WTJ)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PY2CR_PSEUB | Q4U331)
molecular function
    GO:0050132    N-methylalanine dehydrogenase activity    Catalysis of the reaction: N-methyl-L-alanine + H(2)O + NADP(+) = H(+) + methylammonium + NADPH + pyruvate.
    GO:0047125    delta1-piperideine-2-carboxylate reductase activity    Catalysis of the reaction: NADP+ + L-pipecolate = NADPH + delta1-piperideine-2-carboxylate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PY2CR_PSEUB | Q4U331: 2cwf 2cwh

(-) Related Entries Specified in the PDB File

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