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(-) Description

Title :  CRYSTAL STRUCTURE OF NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE FROM BURKHOLDERI PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  17 Mar 09  (Deposition) - 31 Mar 09  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Decode Biostructures, Ssgcid, Niaid, Sbri, Uwppg, Glycosyltransferase, Transferase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Nicotinate-Nucleotide Pyrophosphorylase From Burkholderi Pseudomallei
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE PYROPHOSPHORYLASE
    Chains: A, B
    EC Number: 2.4.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: NADC, BURPS1710B_1132
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B
 
Molecule 2 - UNKNOWN PEPTIDE
    Chains: D, E
    Engineered: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1UNK8Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 3GNN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GNN)

(-) 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:266
 aligned with Q3JV59_BURP1 | Q3JV59 from UniProtKB/TrEMBL  Length:294

    Alignment length:292
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291  
         Q3JV59_BURP1     2 TIDAVSPLFADISREYGAAFDAAIARNVADALAEDVGSGDQTGRLVPDGAPRRARVIVREDAVLCGVPWFDAVVRAVDPSIEVDWRHREGDRMSADSTVCELRGPARALLTAERNALNFLQLLSGVASATRQYVDRIADTRARILDTRKTLPGLRLAQKYAVRVGGGANQRLALYAGILIKENHIAAAGGVGEALDAAFALNAEVPVQIEVETLDQLRTALAHGARSVLLDNFTLDMMRDAVRVTEGRAVLEVSGGVNFDTVRAIAETGVDRISIGALTKDVRATDYSMRIV 293
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----......eeeeeeee...ee..hhhhhhhhhhhhh...eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee........hhhhhhhhhhhh.....-------------------hhhhhhhhhhhhh--...eeee.hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh..eeeeee......hhhhhhhh...eee.hhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gnn A   2 TIDAVSPLFADISREYGAAFDAAIARNVADALAEDVGSG-----LVPDGAPRRARVIVREDAVLCGVPWFDAVVRAVDPSIEVDWRHREGDRMSADSTVCELRGPARALLTAERNALNFLQLLSGVASATRQYVDRIADTRARILDTRKTLPGLRLAQKYAVRVGGGANQ-------------------GVGEALDAAFALN--VPVQIEVETLDQLRTALAHGARSVLLDNFTLDMMRDAVRVTEGRAVLEVSGGVNFDTVRAIAETGVDRISIGALTKDVRATDYSMRIV 293
                                    11        21        31        |-    |   51        61        71        81        91       101       111       121       131       141       151       161       171         -       191       201 |  |  211       221       231       241       251       261       271       281       291  
                                                                 40    46                                                                                                                          171                 191         203  |                                                                                       
                                                                                                                                                                                                                                      206                                                                                       


Chain B from PDB  Type:PROTEIN  Length:244
 aligned with Q3JV59_BURP1 | Q3JV59 from UniProtKB/TrEMBL  Length:294

    Alignment length:290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
         Q3JV59_BURP1     2 TIDAVSPLFADISREYGAAFDAAIARNVADALAEDVGSGDQTGRLVPDGAPRRARVIVREDAVLCGVPWFDAVVRAVDPSIEVDWRHREGDRMSADSTVCELRGPARALLTAERNALNFLQLLSGVASATRQYVDRIADTRARILDTRKTLPGLRLAQKYAVRVGGGANQRLALYAGILIKENHIAAAGGVGEALDAAFALNAEVPVQIEVETLDQLRTALAHGARSVLLDNFTLDMMRDAVRVTEGRAVLEVSGGVNFDTVRAIAETGVDRISIGALTKDVRATDYSMR 291
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...--------.eeeeeeee...ee..hhhhhhhhhhhhh...eeee......ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhh...--------------------------------------.eeee.hhhhhhhhhh....eeee...hhhhhhhhhhhhh....eee.......hhhhhhhh...eeee...........eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gnn B   2 TIDAVSPLFADISREYGAAFDAAIARNVADALAEDVGSGDQ--------APRRARVIVREDAVLCGVPWFDAVVRAVDPSIEVDWRHREGDRMSADSTVCELRGPARALLTAERNALNFLQLLSGVASATRQYVDRIADTRARILDTRKTLPGLRLAQKYAVRVGGGA--------------------------------------VQIEVETLDQLRTALAHGARSVLLDNFTLDMMRDAVRVTEGRAVLEVSGGVNFDTVRAIAETGVDRISIGALTKDVRATDYSMR 291
                                    11        21        31        41|       51        61        71        81        91       101       111       121       131       141       151       161       | -         -         -         -      |211       221       231       241       251       261       271       281       291
                                                                   42       51                                                                                                                   169                                    208                                                                                   


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3gnn D 169 xxxx 172
                            ||||
                          169-UNK
                           170-UNK
                            171-UNK
                             172-UNK


Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3gnn E 181 xxxx 184
                            ||||
                            ||||
                          181-UNK
                           182-UNK
                            183-UNK
                             184-UNK
   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  (0, 0)

(no "SCOP Domain" information available for 3GNN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q3JV59_BURP1 | Q3JV59)
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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