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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BORDETELLA BRONCHISEPTICA ENZYME WBMF IN COMPLEX WITH NAD+ AND UDP
 
Authors :  N. J. Harmer, J. D. King, C. M. Palmer, D. Maskell, T. L. Blundell
Date :  25 May 07  (Deposition) - 02 Oct 07  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Protein-Nad+ Complex, Protein-Udp Complex, 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, B
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
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 , GOL A:801 , HOH A:803 , HOH A:805 , HOH A:823 , HOH A:827 , HOH A:828 , HOH A:829BINDING SITE FOR RESIDUE NAD A 601
2AC2SOFTWAREGLY B:19 , GLY B:22 , PHE B:23 , VAL B:24 , ASP B:44 , ASN B:45 , LEU B:46 , LEU B:47 , SER B:48 , ALA B:49 , SER B:66 , ILE B:67 , LEU B:86 , ALA B:87 , THR B:88 , HIS B:90 , ASN B:105 , THR B:109 , SER B:129 , ALA B:130 , TYR B:161 , LYS B:165 , PHE B:188 , GLN B:189 , ASN B:190 , VAL B:191 , ARG B:212 , GOL B:802 , HOH B:808 , HOH B:809 , HOH B:821 , HOH B:854 , HOH B:855 , HOH B:891BINDING SITE FOR RESIDUE NAD B 602
3AC3SOFTWAREVAL A:214 , PHE A:218 , PRO A:229 , GLU A:231 , ALA A:236 , HOH A:872 , HOH A:994 , HOH A:1048BINDING SITE FOR RESIDUE UDP A 701
4AC4SOFTWAREVAL B:214 , PHE B:218 , PRO B:229 , GLU B:231 , ALA B:236 , ARG B:238 , HOH B:859 , HOH B:965 , HOH B:1010BINDING SITE FOR RESIDUE UDP B 702
5AC5SOFTWAREHIS A:90 , GLY A:91 , ASN A:92 , TYR A:161 , ASN A:213 , NAD A:601 , HOH A:856 , HOH A:902 , HOH A:1040BINDING SITE FOR RESIDUE GOL A 801
6AC6SOFTWAREHIS B:90 , GLY B:91 , ASN B:92 , TYR B:161 , ASN B:213 , NAD B:602 , HOH B:889 , HOH B:890 , HOH B:1008BINDING SITE FOR RESIDUE GOL B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q1U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:90 -Gly A:91
2His B:90 -Gly B:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q1U)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q1U)

(-) 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:336
 aligned with O87989_BORBO | O87989 from UniProtKB/TrEMBL  Length:357

    Alignment length:350
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
         O87989_BORBO     6 NASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAGCSIAEKTFDDAKATEETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeee...hhhhhhhhhhhhhh...eeeee......hhhhh.....eeee.....hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..--------------....eee.....hhhhhhhhhhhhhhhhhhhhhh..eeeee...ee.............hhhhh..hhhhhhhhhhhh......hhhhh.ee..eehhhhhhhhhhhhhhh...eeee......eehhhhhhhhhhhhh......................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1u A   6 NASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAG--------------EETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
                                    15        25        35        45        55        65        75        85        95       105       115       125      |  -         - |     155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
                                                                                                                                                        132            147                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:335
 aligned with O87989_BORBO | O87989 from UniProtKB/TrEMBL  Length:357

    Alignment length:349
                                    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       346         
         O87989_BORBO     7 ASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAGCSIAEKTFDDAKATEETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
               SCOP domains d2q1ub_ B: automated matches                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeeee...hhhhhhhhhhhhhhh..eeeee......hhhhh.....eeee.....hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.--------------....eee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee.............hhhhh..hhhhhhhhhhhh......hhhhh.ee..eehhhhhhhhhhhhhhh...eeee......eehhhhhhhhhhhhh......................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q1u B   7 ASKLANTNVMVVGGAGFVGSNLVKRLLELGVNQVHVVDNLLSAEKINVPDHPAVRFSETSITDDALLASLQDEYDYVFHLATYHGNQSSIHDPLADHENNTLTTLKLYERLKHFKRLKKVVYSAAG--------------EETDIVSLHNNDSPYSMSKIFGEFYSVYYHKQHQLPTVRARFQNVYGPGEILGAGRWRGTPATVWRNVTPTFIYKALKGMPLPLENGGVATRDFIFVEDVANGLIACAADGTPGGVYNIASGKETSIADLATKINEITGNNTELDRLPKRPWDNSGKRFGSPEKARRELGFSADVSIDDGLRKTIEWTKANLAVIEQIMRKHDSALATY 355
                                    16        26        36        46        56        66        76        86        96       106       116       126     |   -         -|      156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346         
                                                                                                                                                       132            147
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Q1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q1U)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  Cis Peptide Bonds
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  2q1u
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2pzj SAME PROTEIN WITHOUT UDP. DIFFERENT CRYSTAL FORM
2q1s SAME PROTEIN WITHOUT UDP, COMPLEXED WITH NADH. DIFFERENT CRYSTAL FORM
2q1t SAME PROTEIN, SOAKED RATHER THAN CO-CRYSTALLISED WITH UDP. DIFFERENT CRYSTAL FORM