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(-) Description

Title :  1.9 ANGSTROM CRYSTAL STRUCTURE OF OROTATE PHOSPHORIBOSYLTRANSFERASE (PYRE) FRANCISELLA TULARENSIS.
 
Authors :  G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  12 Apr 10  (Deposition) - 21 Apr 10  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Orotate, Phosphoribosyltransferase, Idp02311, Csgid, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, L. Shuvalova, I. Dubrovska, J. Winsor, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 9 Angstrom Crystal Structure Of Orotate Phosphoribosyltransferase (Pyre) Francisella Tularensis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - OROTATE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.4.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FTT0437C, FTT_0437C, PYRE
    Organism Scientific: FRANCISELLA TULARENSIS
    Organism Taxid: 119856
    Strain: SCHU S4

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:16 , PHE B:17 , THR B:18 , LYS C:13 , PHE C:28 , ASN C:30 , HOH C:388 , HOH C:561BINDING SITE FOR RESIDUE EDO C 209
2AC2SOFTWAREGLU B:16 , ASN C:9 , LEU C:33 , ASN C:35 , THR C:36 , GLN C:39BINDING SITE FOR RESIDUE TRS C 210

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ala A:65 -Tyr A:66
2Ala B:65 -Tyr B:66
3Ala C:65 -Tyr C:66
4Glu D:-8 -Asn D:-7
5Ala D:65 -Tyr D:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MJD)

(-) 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:209
 aligned with Q5NHL5_FRATT | Q5NHL5 from UniProtKB/TrEMBL  Length:208

    Alignment length:216
                                    1                                                                                                                                                                                                               
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      
         Q5NHL5_FRATT     - --------MFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRKEAKDHGEGGVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKAKDSDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
               SCOP domains d3mjda_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhh....eeee...-------..eee......eeeee......hhhhhhhhhhhhh...eeeeeeeeee..........hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mjd A  -7 NLYFQSNAMFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRKE-------GVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKAKDSDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
                                     2        12        22        32        42        52        62        72        82        92  |      -|      112       122       132       142       152       162       172       182       192       202      
                                                                                                                                 95     103                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with Q5NHL5_FRATT | Q5NHL5 from UniProtKB/TrEMBL  Length:208

    Alignment length:216
                                    1                                                                                                                                                                                                               
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      
         Q5NHL5_FRATT     - --------MFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRKEAKDHGEGGVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKAKDSDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
               SCOP domains d3mjdb_ B: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhh....eeee..--------..eee......eeeee......hhhhhhhhhhhhhh..eeeeeeeeee.....--...hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mjd B  -7 NLYFQSNAMFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRK--------GVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKA--SDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
                                     2        12        22        32        42        52        62        72        82        92 |       -|      112       122       132       142       152  |  | 162       172       182       192       202      
                                                                                                                                94      103                                                 155  |                                                  
                                                                                                                                                                                               158                                                  


Chain C from PDB  Type:PROTEIN  Length:202
 aligned with Q5NHL5_FRATT | Q5NHL5 from UniProtKB/TrEMBL  Length:208

    Alignment length:209
                             1                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199         
         Q5NHL5_FRATT     - -MFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRKEAKDHGEGGVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKAKDSDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
               SCOP domains d3mjdc_ C: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhh....eeee...-------..eee......eeeee......hhhhhhhhhhhhhh..eeeeeeeeee..........hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mjd C   0 AMFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRKE-------GVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKAKDSDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
                                     9        19        29        39        49        59        69        79        89     |   -   |   109       119       129       139       149       159       169       179       189       199         
                                                                                                                          95     103                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:209
 aligned with Q5NHL5_FRATT | Q5NHL5 from UniProtKB/TrEMBL  Length:208

    Alignment length:216
                                    1                                                                                                                                                                                                               
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      
         Q5NHL5_FRATT     - --------MFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRKEAKDHGEGGVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKAKDSDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
               SCOP domains d3mjdd_ D: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------------------Pribosyltran-3mjdD01 D:31-149                                                                                          ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------Pribosyltran-3mjdD02 D:31-149                                                                                          ----------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------Pribosyltran-3mjdD03 D:31-149                                                                                          ----------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------Pribosyltran-3mjdD04 D:31-149                                                                                          ----------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ........hhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh......eeee...-------..eee......eeeee......hhhhhhhhhhhhhh..eeeeeeeeee..........hhhhhhhhhhh..eeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mjd D  -9 TENLYFQAMFIEFALKNQVLKFGEFTLKSGRISPYFFNAGLFNTGAQLATLADYYAQLIIKSDVKYDILFGPAYKGIPLVAAISTVLALKYNIDMPYAFDRKE-------GVFVGADMTNKKVLLIDDVMTAGTAFYESYNKLKIINAKIAGVVLSIDRQEKAKDSDISATKKISQDFNIPVLAVTNFESIFEYVKENLDETMIDKFKQYRQKYGS 208
                                  || 2        12        22        32        42        52        62        72        82        92  |      -|      112       122       132       142       152       162       172       182       192       202      
                                 -3|                                                                                             95     103                                                                                                         
                                   0
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PRTase-like (59)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5NHL5_FRATT | Q5NHL5)
molecular function
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0004588    orotate phosphoribosyltransferase activity    Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
    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:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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  3mjd
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