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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BORDETELLA BRONCHISEPTICA ENZYME WBMF IN COMPLEX WITH NAD+
 
Authors :  N. J. Harmer, J. D. King, C. M. Palmer, D. Maskell, T. L. Blundell
Date :  18 May 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Bordetella Bronchiseptica, Short-Chain Dehydrogenase/Reductase, O Antigen, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. King, N. J. Harmer, A. Preston, C. M. Palmer, M. Rejzek, R. A. Field T. L. Blundell, D. J. Maskell
Predicting Protein Function From Structure--The Roles Of Short-Chain Dehydrogenase/Reductase Enzymes In Bordetella O-Antigen Biosynthesis.
J. Mol. Biol. V. 374 749 2007
PubMed-ID: 17950751  |  Reference-DOI: 10.1016/J.JMB.2007.09.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE NUCLEOTIDE SUGAR EPIMERASE/ DEHYDRATASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BBLPS1.16, WBMF
    Organism Scientific: BORDETELLA BRONCHISEPTICA
    Organism Taxid: 518

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , GLY A:22 , PHE A:23 , VAL A:24 , ASP A:44 , ASN A:45 , LEU A:46 , LEU A:47 , SER A:48 , ALA A:49 , SER A:66 , ILE A:67 , LEU A:86 , ALA A:87 , THR A:88 , HIS A:90 , ASN A:105 , THR A:109 , SER A:129 , ALA A:130 , TYR A:161 , LYS A:165 , PHE A:188 , GLN A:189 , ASN A:190 , VAL A:191 , ARG A:212 , HOH A:363 , HOH A:365 , HOH A:372 , HOH A:395 , HOH A:398 , HOH A:399BINDING SITE FOR RESIDUE NAD A 358

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His A:90 -Gly A:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PZJ)

(-) 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:330
 aligned with O87989_BORBO | O87989 from UniProtKB/TrEMBL  Length:357

    Alignment length:348
                                    17        27        37        47        57        67        77        87        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        
         O87989_BORBO     8 SKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAGCSIAEKTFDDAKATEETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
               SCOP domains d2pzja_ A: automated matches                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh...eeeee......hhhhh.....eeee.....hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.--------------............hhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee.............hhhhh..hhhhhhhhhhhh......hhhhh.ee..eehhhhhhhhhhhhhhh...eeee......eehhhhhhhhhhhhh................----..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pzj A   8 SKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAG--------------EETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNS----GSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
                                    17        27        37        47        57        67        77        87        97       107       117       127    |    -       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297   |   307       317       327       337       347        
                                                                                                                                                      132            147                                                                                                                                                       301  306
   Legend:   → Mismatch (orange background)
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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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (O87989_BORBO | O87989)
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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.

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 Related Entries

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

UniProtKB/TrEMBL
        O87989_BORBO | O87989: 2q1s 2q1t 2q1u

(-) Related Entries Specified in the PDB File

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