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(-) Description

Title :  CRYSTAL STRUCTURE OF A TEREPHTHALATE 1,2-CIS-DIHYDRODIOLDEHYDROGENASE FROM BURKHOLDERIA XENOVORANS LB400
 
Authors :  J. Bains, M. J. Boulanger
Date :  11 May 12  (Deposition) - 22 Aug 12  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bains, J. E. Wulff, M. J. Boulanger
Investigating Terephthalate Biodegradation: Structural Characterization Of A Putative Decarboxylating Cis- Dihydrodiol Dehydrogenase.
J. Mol. Biol. V. 423 284 2012
PubMed-ID: 22889862  |  Reference-DOI: 10.1016/J.JMB.2012.07.022

(-) Compounds

Molecule 1 - TEREPHTHALATE 1,2-CIS-DIHYDRODIOL DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.262
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: BURKHOLDERIA XENOVORANS LB400
    Organism Taxid: 266265
    Synonym: 4-HYDROXYTHREONINE-4-PHOSPHATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:191 , HIS A:235 , HIS A:287 , BME A:1351 , HOH A:2146 , HOH A:2221BINDING SITE FOR RESIDUE ZN A1350
2AC2SOFTWAREHIS A:191 , HIS A:235 , ZN A:1350 , HOH A:2146 , HOH A:2221BINDING SITE FOR RESIDUE BME A1351

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ATY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:109 -Gly A:110
2Gly A:266 -Pro A:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ATY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ATY)

(-) Exons   (0, 0)

(no "Exon" information available for 4ATY)

(-) 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:309
 aligned with Q13RP4_PARXL | Q13RP4 from UniProtKB/TrEMBL  Length:349

    Alignment length:339
                                    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         
         Q13RP4_PARXL     7 RAMTVALAIGDPNGIGPEIAVKAAAQMARDERSEHGGHAVHSQPRIVLFGDAFVIRRYARQCCPELMLRLVQLDDLPSAEPNAIDMVDVASLPAEAFVPGEVAAAAGTATLAYVSAALRAARAGQVDAVIACPHSETAINASGVRFAGYPGFVAHEMGMPAEDVYLLLIGGGLRIVHATLHEGIASALARLDQRHVERAARAAVQALQLMGIAHPVVGLMGINPHAGEGGLFGRDDIDITEPVARKLRDDGMTVIGPQGADLLLTNPDIDVFVAMYHDQGHIPVKLRAGRHSAALSIGAGVLFSSVGHGSGFDIAGTLLADPAPLLGAIRLVTTGTVLA 345
               SCOP domains d4atya_ A: automated matche               s                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......hhhhhhhhhhhh.---------------..-.eeeehhhhhhhhhhhhh--...ee.-----...----.eeee....hhhhh.....hhhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhh---.hhhhhhhhhh..hhhhheeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee..hhhhhh.....hhhhhhhhhhhhhhhhh...eeeeehhhhhh......eeee.hhhhhhhhhhhhhh..eeeeee....eeee................hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aty A  11 RAMTVALAIGDPNGIGPEIAVKAAAQM---------------QP-IVLFGDAFVIRRYARQCC--LMLRLV-----PSA----IDMVDVASLPAEAFVPGEVAAAAGTATLAYVSAALRAARAGQVDAVIACPHSETAINASG---AGYPGFVAHEMGMPAEDVYLLLIGGGLRIVHATLHEGIASALARLDQRHVERAARAAVQALQLMGIAHPVVGLMGINPHAGEGGLFGRDDIDITEPVARKLRDDGMTVIGPQGADLLLTNPDIDVFVAMYHDQGHIPVKLRAGRHSAALSIGAGVLFSSVGHGSGFDIAGTLLADPAPLLGAIRLVTTGTVLA 349
                                    20        30      |  -         -  || |  60        70  |  |  80|     | |-   |   100       110       120       130       140       150  |   |160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340         
                                                     37              53| |               73 76   81    87 |   94                                                        153 157                                                                                                                                                                                                
                                                                      54 |                               89                                                                                                                                                                                                                                                                    
                                                                        56
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ATY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ATY)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q13RP4_PARXL | Q13RP4)
molecular function
    GO:0050570    4-hydroxythreonine-4-phosphate dehydrogenase activity    Catalysis of the reaction: 4-(phosphonooxy)-threonine + NAD+ = 2-amino-3-oxo-4-phosphonooxybutyrate + NADH + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
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.
    GO:0008615    pyridoxine biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.

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