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(-) Description

Title :  CRYSTAL STRUCTURE OF A NICOTINATE NUCLEOTIDE PYROPHOSPHORYLASE (TM1645) FROM THERMOTOGA MARITIMA AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Jul 03  (Deposition) - 22 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Schwarzenbacher, L. Jaroszewski, F. Von Delft, P. Abdubek, E. Ambing, T. Biorac, L. S. Brinen, J. M. Canaves, J. Cambell, H. J. Chiu X. Dai, A. M. Deacon, M. Didonato, M. A. Elsliger, S. Eshagi, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, E. Hampton, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, S. A. Lesley I. Levin, D. Mcmullan, T. M. Mcphillips, M. D. Miller, A. Morse, K. Moy, J. Ouyang, R. Page, K. Quijano, A. Robb, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, X. Wang, B. West, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of A Type Ii Quinolic Acid Phosphoribosyltransferase (Tm1645) From Thermotoga Maritima At 2. 50 A Resolution
Proteins V. 55 768 2004
PubMed-ID: 15103640  |  Reference-DOI: 10.1002/PROT.20029

(-) Compounds

Molecule 1 - TYPE II QUINOLIC ACID PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1645
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1O4U)

(-) Sites  (0, 0)

(no "Site" information available for 1O4U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O4U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:16 -Gly A:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O4U)

(-) Exons   (0, 0)

(no "Exon" information available for 1O4U)

(-) 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:265
 aligned with Q9X1X8_THEMA | Q9X1X8 from UniProtKB/TrEMBL  Length:273

    Alignment length:273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
         Q9X1X8_THEMA     1 MEKILDLLMSFVKEDEGKLDLASFPLRNTTAGAHLLLKTENVVASGIEVSRMFLEKMGLLSKFNVEDGEYLEGTGVIGEIEGNTYKLLVAERTLLNVLSVMFSVATTTRRFAEKLKHAKIAATRKILPGLGVLQKIAVVHGGGDPHRLDLSGCVMIKDNHLKMYGSAERAVQEVRKIIPFTTKIEVEVENLEDALRAVEAGADIVMLDNLSPEEVKDISRRIKDINPNVIVEVSGGITEENVSLYDFETVDVISSSRLTLQEVFVDLSLEIQR 273
               SCOP domains d1o4ua2 A:1-103                                                                                        d1o4ua1 A:104-273 Quinolinic acid phospho        ribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain                                     SCOP domains
               CATH domains 1o4uA01 A:1-106,A:262-273  [code=3.90.1170.20, no name defined]                                           1o4uA02 A:107-261 Aldolase class I                                                                                                                         1o4uA01      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhh..eeeeeeee...eee..hhhhhhhhhhhh..eeee......eee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhh..--------.eeehhhhhhh...hhhhhhhhhh.......eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...eeeeee.....hhhhhh.....eeeehhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o4u A   1 MEKILDLLMSFVKEDEGKLDLASFPLRNTTAGAHLLLKTENVVASGIEVSRMFLEKMGLLSKFNVEDGEYLEGTGVIGEIEGNTYKLLVAERTLLNVLSVMFSVATTTRRFAEKLKHAKIAATRKILPGLGVLQKIAVVHGGGD--------CVMIKDNHLKMYGSAERAVQEVRKIIPFTTKIEVEVENLEDALRAVEAGADIVMLDNLSPEEVKDISRRIKDINPNVIVEVSGGITEENVSLYDFETVDVISSSRLTLQEVFVDLSLEIQR 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   |     -  |    160       170       180       190       200       210       220       230       240       250       260       270   
                                                                                                                                                                         144      153                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with Q9X1X8_THEMA | Q9X1X8 from UniProtKB/TrEMBL  Length:273

    Alignment length:273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   
         Q9X1X8_THEMA     1 MEKILDLLMSFVKEDEGKLDLASFPLRNTTAGAHLLLKTENVVASGIEVSRMFLEKMGLLSKFNVEDGEYLEGTGVIGEIEGNTYKLLVAERTLLNVLSVMFSVATTTRRFAEKLKHAKIAATRKILPGLGVLQKIAVVHGGGDPHRLDLSGCVMIKDNHLKMYGSAERAVQEVRKIIPFTTKIEVEVENLEDALRAVEAGADIVMLDNLSPEEVKDISRRIKDINPNVIVEVSGGITEENVSLYDFETVDVISSSRLTLQEVFVDLSLEIQR 273
               SCOP domains d1o4ub2 B:1-103                                                                                        d1o4ub1 B:104-273 Quinolinic acid phospho       ribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain                                      SCOP domains
               CATH domains 1o4uB01 B:1-106,B:262-273  [code=3.90.1170.20, no name defined]                                           1o4uB02 B:107-261 Aldolase class I                                                                                                                         1o4uB01      CATH domains
           Pfam domains (1) ---------------QRPTase_N-1o4uB01 B:16-102                                                             -QRPTase_C-1o4uB03 B:104-270                                                                                                                                            --- Pfam domains (1)
           Pfam domains (2) ---------------QRPTase_N-1o4uB02 B:16-102                                                             -QRPTase_C-1o4uB04 B:104-270                                                                                                                                            --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhh..eeeeeeee...eee..hhhhhhhhhhhhh.eeee......eee..eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhh..-------.eeeehhhhhhh...hhhhhhhhhh......eeeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...eeeeee.....hhhhhh.....eeeehhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o4u B   1 MEKILDLLMSFVKEDEGKLDLASFPLRNTTAGAHLLLKTENVVASGIEVSRMFLEKMGLLSKFNVEDGEYLEGTGVIGEIEGNTYKLLVAERTLLNVLSVMFSVATTTRRFAEKLKHAKIAATRKILPGLGVLQKIAVVHGGGD-------GCVMIKDNHLKMYGSAERAVQEVRKIIPFTTKIEVEVENLEDALRAVEAGADIVMLDNLSPEEVKDISRRIKDINPNVIVEVSGGITEENVSLYDFETVDVISSSRLTLQEVFVDLSLEIQR 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140   |     - |     160       170       180       190       200       210       220       230       240       250       260       270   
                                                                                                                                                                         144     152
   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  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Hybrid (58)
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9X1X8_THEMA | Q9X1X8)
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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    Glu A:16 - Gly A:17   [ RasMol ]  
 

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