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(-) Description

Title :  CRYSTAL STRUCTURE OF NICOTINATE PHOSPHORIBOSYLTRANSFERASE FROM PORPHYROMONAS GINGIVALIS
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  03 Oct 06  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Nysgxrc, Phosphoribosyltransferase, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Nicotinate Phosphoribosyltransferase From Porphyromonas Gingivalis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICOTINATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PNCB
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 837

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2IM5)

(-) Sites  (0, 0)

(no "Site" information available for 2IM5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IM5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IM5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IM5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IM5)

(-) Exons   (0, 0)

(no "Exon" information available for 2IM5)

(-) 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:389
 aligned with Q7MXV0_PORGI | Q7MXV0 from UniProtKB/TrEMBL  Length:394

    Alignment length:389
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         
         Q7MXV0_PORGI     3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
               SCOP domains d2im5a1 A:3-137 Nicotinate phosphoribosyltransferase, N-terminal domain                                                                d2im5a2 A:138-391 Nicotinate phosphoribosyltransferase, C-terminal domain                                                                                                                                                                                      SCOP domains
               CATH domains 2im5A00 A:3-391 nicotinate phosphoribosyltransferase                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh..hhh.eeeee.....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh...eeee.hhhhhhhhh.ee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh..hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh..........eeeeeeeee.......ee.............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2im5 A   3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with Q7MXV0_PORGI | Q7MXV0 from UniProtKB/TrEMBL  Length:394

    Alignment length:389
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         
         Q7MXV0_PORGI     3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
               SCOP domains d2im5b1 B:3-137 Nicotinate phosphoribosyltransferase, N-terminal domain                                                                d2im5b2 B:138-391 Nicotinate phosphoribosyltransferase, C-terminal domain                                                                                                                                                                                      SCOP domains
               CATH domains 2im5B00 B:3-391 nicotinate phosphoribosyltransferase                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh..hhh.eeeee.....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh...eeee.hhhhhhhhh.ee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh..hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh..........eeeeeeeee.......ee.............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2im5 B   3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         


Chain C from PDB  Type:PROTEIN  Length:389
 aligned with Q7MXV0_PORGI | Q7MXV0 from UniProtKB/TrEMBL  Length:394

    Alignment length:389
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         
         Q7MXV0_PORGI     3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
               SCOP domains d2im5c1 C:3-137 Nicotinate phosphoribosyltransferase, N-terminal domain                                                                d2im5c2 C:138-391 Nicotinate phosphoribosyltransferase, C-terminal domain                                                                                                                                                                                      SCOP domains
               CATH domains 2im5C00 C:3-391 nicotinate phosphoribosyltransferase                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh..hhh.eeeee.....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh...eeee.hhhhhhhhh.ee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh..hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh..........eeeeeeeee.......ee.............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2im5 C   3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         


Chain D from PDB  Type:PROTEIN  Length:389
 aligned with Q7MXV0_PORGI | Q7MXV0 from UniProtKB/TrEMBL  Length:394

    Alignment length:389
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382         
         Q7MXV0_PORGI     3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
               SCOP domains d2im5d1 D:3-137 Nicotinate phosphoribosyltransferase, N-terminal domain                                                                d2im5d2 D:138-391 Nicotinate phosphoribosyltransferase, C-terminal domain                                                                                                                                                                                      SCOP domains
               CATH domains 2im5D00 D:3-391 nicotinate phosphoribosyltransferase                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh..hhh.eeeee.....eeeeeeeehhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhh...eeee.hhhhhhhhh.ee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhh..hhhh.eeee....hhhhhhhhhhhhh...eeeeeehhhhhh..........eeeeeeeee.......ee.............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2im5 D   3 IIRSILDTDLYKFTTGYAYAKLFPRAYGEFRFIDRNRQGFTEEFAELVRGEIRAMAALSLTRDEKEFLQRELPYLPPIYIDFLDGFRFDPEEVTVSIDAQGHLDIRAQGLLYRVTLWETPILAVISELYYRFIGAEPDWKQVEEVTRSKGELMREHRATFSIFGMRRRFSLEVEDRVTDILKQYAGESLFGTSNVHLAHKHGLRVSGTHPHEWIQFHGAIYGYKMANYVAMEDWINVYDGDLGTVLTDTYTTDVFMRNFSKKHAMLFTSLRHDSGDPEIFIEKAVRRYEELRVDPKIKYIIFSDSLTPQRAIEIQKLCAGRIKASFGIGTNLTNDVGGGVEPLNIVMKLWKCKMTAKDDWHYCVKLSDVDGKHTGEPEEILLAMNTLGI 391
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382
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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  (2, 8)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IM5)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7MXV0_PORGI | Q7MXV0)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0004516    nicotinate phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + nicotinate D-ribonucleotide = 5-phospho-alpha-D-ribose 1-diphosphate + H(+) + nicotinate.
    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).
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:0019357    nicotinate nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide nucleotides, any nucleotide that contains combined nicotinate (pyridine 3-carboxylic acid).
    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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