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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BORDETELLA BRONCHISEPTICA ENZYME WBMG IN COMPLEX WITH NAD AND UDP
 
Authors :  J. D. King, N. J. Harmer, D. J. Maskell, T. L. Blundell
Date :  18 May 07  (Deposition) - 02 Oct 07  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Protein-Nad Complex, Protein-Nucleotide 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: BBLPS1.15, WBMG
    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  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , ALA A:9 , GLY A:10 , CYS A:11 , LEU A:12 , ASP A:31 , ASN A:32 , PHE A:33 , ALA A:34 , THR A:35 , GLY A:36 , GLY A:52 , SER A:53 , VAL A:54 , SER A:75 , ALA A:76 , ALA A:77 , TYR A:79 , THR A:91 , PHE A:114 , GLN A:115 , THR A:116 , TYR A:140 , LYS A:144 , ALA A:164 , VAL A:166 , HOH A:418 , HOH A:462 , HOH A:483BINDING SITE FOR RESIDUE NAD A 401
2AC2SOFTWAREGLY B:7 , ALA B:9 , GLY B:10 , CYS B:11 , LEU B:12 , ASP B:31 , ASN B:32 , PHE B:33 , ALA B:34 , THR B:35 , GLY B:36 , GLY B:52 , SER B:53 , VAL B:54 , SER B:75 , ALA B:76 , ALA B:77 , TYR B:79 , THR B:91 , PHE B:114 , GLN B:115 , TYR B:140 , LYS B:144 , ALA B:164 , ASN B:165 , VAL B:166 , HOH B:409 , HOH B:427BINDING SITE FOR RESIDUE NAD B 401
3AC3SOFTWAREPRO A:175 , PHE A:190 , CYS A:191 , SER A:192 , THR A:194 , ILE A:231 , ASP A:259 , HOH A:405BINDING SITE FOR RESIDUE UDP A 402
4AC4SOFTWARETHR B:178 , PHE B:179 , PHE B:190 , CYS B:191 , SER B:192 , THR B:194 , ILE B:231 , ASP B:259 , HOH B:456BINDING SITE FOR RESIDUE UDP B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:126 -Pro A:127
2Val B:-5 -Pro B:-4
3Val B:126 -Pro B:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PZL)

(-) 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:310
 aligned with O87988_BORBO | O87988 from UniProtKB/TrEMBL  Length:310

    Alignment length:310
                              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       268       278       288       298       308
         O87988_BORBO     - --MRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGATLAEPVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLSAP 308
               SCOP domains d2pzla_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh.eeeeee.....hhhhh.....eeeee....hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhh.....eeeeee.eee......hhhhhhhhhhhh.....ee..ee.eeehhhhhhhhhhhh......eeeee.....eehhhhhhhhhhhhh........ee........ee...hhhhhhhhh.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzl A  -1 SHMRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGATLAEPVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLSAP 308
                                     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       268       278       288       298       308


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with O87988_BORBO | O87988 from UniProtKB/TrEMBL  Length:310

    Alignment length:313
                                   1                                                                                                                                                                                                                                                                                                                 
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303   
         O87988_BORBO     - -------MRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGATLAEPVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLS 306
               SCOP domains d2pzlb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhhh.eeeeee.....hhhhh.....eeeee....hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhh.....eeeeee.eee......hhhhhhhhhhhh.....ee..ee.eeehhhhhhhhhhhh......eeeee.....eehhhhhhhhhhhhh.----...ee.............hhhhhhhhh.....hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzl B  -6 LVPRGSHMRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGA----PVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLS 306
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243|    | 253       263       273       283       293       303   
                                                                                                                                                                                                                                                                                    244  249
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O87988_BORBO | O87988)
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
        O87988_BORBO | O87988: 2pzk 2pzm

(-) Related Entries Specified in the PDB File

2pzk THE SAME PROTEIN IN THE ABSENCE OF NUCLEOTIDE; IDENTICAL CRYSTAL FORM.