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(-) Description

Title :  STRUCTURE OF THE NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE FROM FRANCISELLA TULARENSIS.
 
Authors :  M. Rudolph, J. Cheung, M. Franklin, M. Cassidy, E. Gary, F. Burshteyn, J
Date :  09 Sep 11  (Deposition) - 28 Sep 11  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chaudhury, M. D. Abdulhameed, N. Singh, G. J. Tawa, P. M. D'Haeseleer, A. T. Zemla, A. Navid, C. E. Zhou, M. C. Franklin, J. Cheung, M. J. Rudolph, J. Love, J. F. Graf, D. A. Rozak, J. L. Dankmeyer, K. Amemiya, S. Daefler, A. Wallqvist
Rapid Countermeasure Discovery Against Francisella Tularensis Based On A Metabolic Network Reconstruction.
Plos One V. 8 63369 2013
PubMed-ID: 23704901  |  Reference-DOI: 10.1371/JOURNAL.PONE.0063369

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE
    Chains: A, B
    EC Number: 2.4.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NADC, FTT_1468C
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 177416
    Strain: SCHU S4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:141 , ARG A:142 , HIS A:164 , ARG A:165 , LEU A:173 , LYS A:175 , HOH A:300 , HOH A:363BINDING SITE FOR RESIDUE PO4 A 288
2AC2SOFTWARELYS A:143 , ASN A:250 , GLY A:270 , LYS A:274 , HOH A:290BINDING SITE FOR RESIDUE PO4 A 289
3AC3SOFTWARELYS B:143 , ASN B:250 , GLY B:270 , LYS B:274 , HOH B:292 , HOH B:298 , HOH B:308BINDING SITE FOR RESIDUE PO4 B 288
4AC4SOFTWARETHR B:141 , ARG B:142 , HIS B:164 , ARG B:165 , LEU B:173 , HOH B:290 , HOH B:291BINDING SITE FOR RESIDUE PO4 B 289

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TQV)

(-) 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:276
 aligned with Q5NEY8_FRATT | Q5NEY8 from UniProtKB/TrEMBL  Length:287

    Alignment length:280
                                    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
         Q5NEY8_FRATT     7 NTDQINKVPNDIVTRLVRESLAEDIATGDITAQLAEDIDTTAFCITREEMILCGQDFANEVINQLDKNIQITWLYSDAQKVPANARIFELKGNVRSILTAERTILNFIQMLSGTATVTNKLVKLISQYKTKLLDTRKTIPGFRLAQKYAVRCGGGFNHRIGLFDAYLIKENHIRSAGGIAKAVTKAKKLDSNKVVEVEVTNLDELNQAIAAKADIVMLDNFSGEDIDIAVSIARGKVALEVSGNIDRNSIVAIAKTGVDFISVGAITKHIKAIDLSLQVQ 286
               SCOP domains d3tqva1 A:7-119 automated matches                                                                                d3tqva2 A:120-286 automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh..hhhhhhh...eeeeeeee...ee..hhhhhhhhhhhhh...eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eee.....----.hhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee......hhhhhhh....eee.hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqv A   7 NTDQINKVPNDIVTRLVRESLAEDIATGDITAQLAEDIDTTAFCITREEmILCGQDFANEVINQLDKNIQITWLYSDAQKVPANARIFELKGNVRSILTAERTILNFIQmLSGTATVTNKLVKLISQYKTKLLDTRKTIPGFRLAQKYAVRCGGGFNHRIGLFDAYLIKENHI----GIAKAVTKAKKLDSNKVVEVEVTNLDELNQAIAAKADIVmLDNFSGEDIDIAVSIARGKVALEVSGNIDRNSIVAIAKTGVDFISVGAITKHIKAIDLSLQVQ 286
                                    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
                                                                            56-MSE                                                     116-MSE                                                        179  184                                    223-MSE                                                           


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with Q5NEY8_FRATT | Q5NEY8 from UniProtKB/TrEMBL  Length:287

    Alignment length:280
                                    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
         Q5NEY8_FRATT     7 NTDQINKVPNDIVTRLVRESLAEDIATGDITAQLAEDIDTTAFCITREEMILCGQDFANEVINQLDKNIQITWLYSDAQKVPANARIFELKGNVRSILTAERTILNFIQMLSGTATVTNKLVKLISQYKTKLLDTRKTIPGFRLAQKYAVRCGGGFNHRIGLFDAYLIKENHIRSAGGIAKAVTKAKKLDSNKVVEVEVTNLDELNQAIAAKADIVMLDNFSGEDIDIAVSIARGKVALEVSGNIDRNSIVAIAKTGVDFISVGAITKHIKAIDLSLQVQ 286
               SCOP domains d3tqvb1 B:7-119 automated matches                                                                                d3tqvb2 B:120-286 automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh....hhhhh...eeeeeeee...ee..hhhhhhhhhhhhh...eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhh...........eeeehhhhhhh..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee......hhhhhhh....eee.hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqv B   7 NTDQINKVPNDIVTRLVRESLAEDIATGDITAQLAEDIDTTAFCITREEmILCGQDFANEVINQLDKNIQITWLYSDAQKVPANARIFELKGNVRSILTAERTILNFIQmLSGTATVTNKLVKLISQYKTKLLDTRKTIPGFRLAQKYAVRCGGGFNHRIGLFDAYLIKENHIRSAGGIAKAVTKAKKLDSNKVVEVEVTNLDELNQAIAAKADIVmLDNFSGEDIDIAVSIARGKVALEVSGNIDRNSIVAIAKTGVDFISVGAITKHIKAIDLSLQVQ 286
                                    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
                                                                            56-MSE                                                     116-MSE                                                                                                    223-MSE
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5NEY8_FRATT | Q5NEY8)
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:0004514    nicotinate-nucleotide diphosphorylase (carboxylating) activity    Catalysis of the reaction: CO(2) + diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+) + quinolinate.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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