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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI NUCLEOSIDE PHOSPHORYLASE SHOWS URIDINE PHOSPHORYLASE ACTIVITY
 
Authors :  E. T. Larson, E. A. Merritt, Structural Genomics Of Pathogenic Pro Consortium (Sgpp)
Date :  03 Dec 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleoside Phosphorylase, Uridine Phosphorylase, Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa Consortium, Msgpp, Trypanosoma, Brucei, Sleeping Sickness, Glycosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. T. Larson, D. G. Mudeppa, J. R. Gillespie, N. Mueller, A. J. Napuli, J. A. Arif, J. Ross, T. L. Arakaki, A. Lauricella, G. Detitta, J. Luft, F. Zucker, C. L. Verlinde, E. Fan, W. C. Van Voorhis, F. S. Buckner, P. K. Rathod, W. G. Hol, E. A. Merritt
The Crystal Structure And Activity Of A Putative Trypanosomal Nucleoside Phosphorylase Reveal It To Be A Homodimeric Uridine Phosphorylase
J. Mol. Biol. V. 396 1244 2010
PubMed-ID: 20070944  |  Reference-DOI: 10.1016/J.JMB.2010.01.013

(-) Compounds

Molecule 1 - NUCLEOSIDE PHOSPHORYLASE, PUTATIVE
    Chains: A, B
    EC Number: 2.4.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BG1861
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TB927.8.4430
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Strain: GUTAT10.1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2R1P2Ligand/IonRIBOSE-1-PHOSPHATE
3URA2Ligand/IonURACIL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:42 , ASP A:43 , ARG A:46 , MET A:87 , ARG A:137 , GLY A:139 , THR A:140 , GLU A:284 , MET A:285 , GLU A:286 , URA A:501 , HOH A:605 , HIS B:26 , ARG B:66BINDING SITE FOR RESIDUE R1P A 401
2AC2SOFTWARECYS A:141 , GLY A:142 , PHE A:242 , GLN A:246 , ARG A:248 , GLU A:284 , MET A:285 , SER A:309 , R1P A:401 , HOH A:543BINDING SITE FOR RESIDUE URA A 501
3AC3SOFTWAREHIS A:26 , ARG A:66 , GLY B:42 , ASP B:43 , ARG B:46 , MET B:87 , ARG B:137 , GLY B:139 , THR B:140 , GLU B:284 , MET B:285 , GLU B:286 , URA B:501 , HOH B:617BINDING SITE FOR RESIDUE R1P B 401
4AC4SOFTWARECYS B:141 , GLY B:142 , PHE B:242 , GLN B:246 , ARG B:248 , ILE B:283 , GLU B:284 , MET B:285 , SER B:309 , R1P B:401 , HOH B:526BINDING SITE FOR RESIDUE URA B 501
5AC5SOFTWAREMET A:87 , ASP A:90 , ASN A:91 , MET B:87 , ASP B:90 , ASN B:91BINDING SITE FOR RESIDUE CA B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:125 -Pro A:126
2Gly B:125 -Pro B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BJE)

(-) 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:327
 aligned with Q57VZ2_TRYB2 | Q57VZ2 from UniProtKB/TrEMBL  Length:341

    Alignment length:327
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       
         Q57VZ2_TRYB2    15 DLPIGKDGTTLHLKCKSDELADRIIFVGDPGRVDVISGYFDKDSIRASRDHREIRFATGTYKGTPVTVISTGMGVDNIEIVLNEIHALKEYDMERGQWRHRKGDADAPSAGPFFDPSTMKIIRLGTCGSPAESVPPLALAVTRHAIGMDNTSLYYSAGTRETSKDQQEIRRIVREQTGLRAIDIYTSMAHPNITKSICAACDAHNAATGSEADKQQYVIGTTATASGFYGCQGRRVGRFMKHLTVPNMVEELGSLKFNLSNGVEVVTNIEMETSAICYLSDMLGYQAGAACVVVSKRVGEKKMFLGDQLDAAMKRCIKIILEALVSA 341
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------3bjeA01 A:30-341  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh..eeeee...hhhhhhhh........eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhee....ee................hhhh.eeeeeeeeee.........eeeeeeeee..hhhhhhh......hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh..hhhhh..eeeeeeee....hhhhh..hhhhhhhh...hhhhhhhhh.eee..eee.eeeee.hhhhhhhhhhhhh.eeeeeeeeeee.....ee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bje A  15 DLPIGKDGTTLHLKCKSDELADRIIFVGDPGRVDVISGYFDKDSIRASRDHREIRFATGTYKGTPVTVISTGMGVDNIEIVLNEIHALKEYDMERGQWRHRKGDADAPSAGPFFDPSTMKIIRLGTCGSPAESVPPLALAVTRHAIGMDNTSLYYSAGTRETSKDQQEIRRIVREQTGLRAIDIYTSMAHPNITKSICAACDAHNAATGSEADKQQYVIGTTATASGFYGCQGRRVGRFMKHLTVPNMVEELGSLKFNLSNGVEVVTNIEMETSAICYLSDMLGYQAGAACVVVSKRVGEKKMFLGDQLDAAMKRCIKIILEALVSA 341
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with Q57VZ2_TRYB2 | Q57VZ2 from UniProtKB/TrEMBL  Length:341

    Alignment length:327
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       
         Q57VZ2_TRYB2    15 DLPIGKDGTTLHLKCKSDELADRIIFVGDPGRVDVISGYFDKDSIRASRDHREIRFATGTYKGTPVTVISTGMGVDNIEIVLNEIHALKEYDMERGQWRHRKGDADAPSAGPFFDPSTMKIIRLGTCGSPAESVPPLALAVTRHAIGMDNTSLYYSAGTRETSKDQQEIRRIVREQTGLRAIDIYTSMAHPNITKSICAACDAHNAATGSEADKQQYVIGTTATASGFYGCQGRRVGRFMKHLTVPNMVEELGSLKFNLSNGVEVVTNIEMETSAICYLSDMLGYQAGAACVVVSKRVGEKKMFLGDQLDAAMKRCIKIILEALVSA 341
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------3bjeB01 B:30-341  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhh..eeeee...hhhhhhhh........eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhhee....ee................hhhh.eeeeeeeeee.........eeeeeeeee..hhhhhhh......hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh..hhhhh..eeeeeeee....hhhhh..hhhhhhhh...hhhhhhhh..eee..eee.eeeee.hhhhhhhhhhhhh.eeeeeeeeeee.....ee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bje B  15 DLPIGKDGTTLHLKCKSDELADRIIFVGDPGRVDVISGYFDKDSIRASRDHREIRFATGTYKGTPVTVISTGMGVDNIEIVLNEIHALKEYDMERGQWRHRKGDADAPSAGPFFDPSTMKIIRLGTCGSPAESVPPLALAVTRHAIGMDNTSLYYSAGTRETSKDQQEIRRIVREQTGLRAIDIYTSMAHPNITKSICAACDAHNAATGSEADKQQYVIGTTATASGFYGCQGRRVGRFMKHLTVPNMVEELGSLKFNLSNGVEVVTNIEMETSAICYLSDMLGYQAGAACVVVSKRVGEKKMFLGDQLDAAMKRCIKIILEALVSA 341
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
   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 3BJE)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q57VZ2_TRYB2 | Q57VZ2)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004731    purine-nucleoside phosphorylase activity    Catalysis of the reaction: purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.
    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:0004850    uridine phosphorylase activity    Catalysis of the reaction: uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
biological process
    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).

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