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(-) Description

Title :  CRYSTAL STRUCTURE OF URONATE DEHYDROGENASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  T. Parkkinen, J. Rouvinen
Date :  07 Apr 11  (Deposition) - 15 Jun 11  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Apoenzyme, Rossmann Fold, Nad Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Parkkinen, H. Boer, J. Janis, M. Andberg, M. Penttila, A. Koivula, J. Rouvinen
Crystal Structure Of Uronate Dehydrogenase From Agrobacterium Tumefaciens.
J. Biol. Chem. V. 286 27294 2011
PubMed-ID: 21676870  |  Reference-DOI: 10.1074/JBC.M111.254854

(-) Compounds

Molecule 1 - URONATE DEHYDROGENASE
    Chains: A, B, C
    EC Number: 1.1.1.203
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Taxid: 4932
    Gene: UDH, AGR_L_3333, ATU3143
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 176299
    Strain: C58 / ATCC 33970

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric Unit (1, 15)
No.NameCountTypeFull Name
1SO415Ligand/IonSULFATE ION
Biological Unit 1 (1, 30)
No.NameCountTypeFull Name
1SO430Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:4 , ARG A:5BINDING SITE FOR RESIDUE SO4 A 268
02AC2SOFTWAREARG A:22 , HIS A:182BINDING SITE FOR RESIDUE SO4 A 269
03AC3SOFTWAREASN A:112 , HIS A:113 , GLY A:164 , SER A:165 , ARG A:174 , HOH A:473 , HOH A:610 , HOH A:640 , HOH A:657BINDING SITE FOR RESIDUE SO4 A 270
04AC4SOFTWAREARG A:148 , PHE A:151 , HOH A:330 , HOH A:411 , HOH A:598BINDING SITE FOR RESIDUE SO4 A 271
05AC5SOFTWAREGLY B:64 , HIS B:101 , HOH B:551 , HOH B:688BINDING SITE FOR RESIDUE SO4 B 268
06AC6SOFTWARELYS B:4 , ARG B:5BINDING SITE FOR RESIDUE SO4 B 269
07AC7SOFTWAREARG B:22 , HIS B:182 , ASP B:183 , HOH B:320BINDING SITE FOR RESIDUE SO4 B 270
08AC8SOFTWARELYS B:78 , GLN B:82 , GLN B:266 , HOH B:616 , HOH B:762BINDING SITE FOR RESIDUE SO4 B 271
09AC9SOFTWAREASN B:112 , HIS B:113 , GLY B:164 , SER B:165 , ARG B:174 , HOH B:368 , HOH B:419 , HOH B:433 , HOH B:567BINDING SITE FOR RESIDUE SO4 B 272
10BC1SOFTWAREARG B:148 , PHE B:151 , HOH B:339 , HOH B:556 , HOH B:614 , HOH B:776BINDING SITE FOR RESIDUE SO4 B 273
11BC2SOFTWARELYS C:4 , ARG C:5 , HOH C:629BINDING SITE FOR RESIDUE SO4 C 268
12BC3SOFTWAREALA C:63 , GLY C:64 , HIS C:101 , HOH C:548BINDING SITE FOR RESIDUE SO4 C 269
13BC4SOFTWAREARG C:22 , HIS C:182BINDING SITE FOR RESIDUE SO4 C 270
14BC5SOFTWAREASN C:112 , HIS C:113 , GLY C:164 , SER C:165 , ARG C:174 , HOH C:355 , HOH C:442 , HOH C:461 , HOH C:550 , HOH C:783BINDING SITE FOR RESIDUE SO4 C 271
15BC6SOFTWAREARG C:148 , PHE C:151 , HOH C:334 , HOH C:389 , HOH C:521BINDING SITE FOR RESIDUE SO4 C 272

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RFT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RFT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RFT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RFT)

(-) Exons   (0, 0)

(no "Exon" information available for 3RFT)

(-) 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:266
 aligned with URODH_AGRFC | Q7CRQ0 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:266
                              1                                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          URODH_AGRFC     - --MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 264
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhh...eeeeeeee..........eeeee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhh.hhhhhhhhhhhhhhh......eeee..........hhhhhhhh.....hhhhhhhhhhh........hhhhh..hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rft A   1 MAMKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with URODH_AGRFC | Q7CRQ0 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:266
                              1                                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          URODH_AGRFC     - --MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 264
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhh...eeeeeeee..........eeeee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhh.hhhhhhhhhhhhhhh......eeee..........hhhhhhhh.....hhhhhhhhhhhhh......hhhhh..hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rft B   1 MAMKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      


Chain C from PDB  Type:PROTEIN  Length:266
 aligned with URODH_AGRFC | Q7CRQ0 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:266
                              1                                                                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          URODH_AGRFC     - --MKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 264
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhh...eeeeeeee..........eeeee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhh.hhhhhhhhhhhhhhh......eeee..........hhhhhhhh.....hhhhhhhhhhhhh......hhhhh..hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rft C   1 MAMKRLLVTGAAGQLGRVMRERLAPMAEILRLADLSPLDPAGPNEECVQCDLADANAVNAMVAGCDGIVHLGGISVEKPFEQILQGNIIGLYNLYEAARAHGQPRIVFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARMYFDKFGQETALVRIGSCTPEPNNYRMLSTWFSHDDFVSLIEAVFRAPVLGCPVVWGASANDAGWWDNSHLGFLGWKPKDNAEAFRRHITETTPPPDPNDALVRFQGGTFVDNPIFKQ 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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  (0, 0)

(no "SCOP Domain" information available for 3RFT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RFT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RFT)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (URODH_AGRFC | Q7CRQ0)
molecular function
    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:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    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.
    GO:0050388    uronate dehydrogenase activity    Catalysis of the reaction: D-galacturonate + H(2)O + NAD(+) = galactarate + 2 H(+) + NADH.
biological process
    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

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        URODH_AGRFC | Q7CRQ0: 3rfv 3rfx

(-) Related Entries Specified in the PDB File

3rfv 3rfx