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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PURINE NUCLEOSIDE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH PHOSPHATE AND ACETATE
 
Authors :  H. D. Pereira, G. R. Franco, A. Cleasby, R. C. Garratt
Date :  21 May 04  (Deposition) - 24 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Purine Nucleoside Phosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. D. Pereira, G. R. Franco, A. Cleasby, R. C. Garratt
Structures For The Potential Drug Target Purine Nucleoside Phosphorylase From Schistosoma Mansoni Causal Agent Of Schistosomiasis.
J. Mol. Biol. V. 353 584 2005
PubMed-ID: 16182308  |  Reference-DOI: 10.1016/J.JMB.2005.08.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PURINE-NUCLEOSIDE PHOSPHORYLASE
    Chains: A, B, C
    EC Number: 2.4.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL C2G
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SMPNP
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:119 , GLY A:120 , TYR A:202 , GLU A:203 , VAL A:219 , GLY A:220 , MET A:221 , ASN A:245 , HOH A:726 , HOH A:799BINDING SITE FOR RESIDUE ACT A 700
2AC2SOFTWAREALA B:119 , GLY B:120 , TYR B:202 , GLU B:203 , VAL B:219 , GLY B:220 , MET B:221 , ASN B:245 , HOH B:794BINDING SITE FOR RESIDUE ACT B 701
3AC3SOFTWAREALA C:119 , GLY C:120 , TYR C:202 , GLU C:203 , VAL C:219 , GLY C:220 , MET C:221 , ASN C:245 , HOH C:716 , HOH C:756BINDING SITE FOR RESIDUE ACT C 702
4AC4SOFTWAREGLY A:34 , SER A:35 , ARG A:86 , HIS A:88 , ASN A:117 , ALA A:118 , SER A:222 , HOH A:806 , HOH A:830 , HOH A:852 , HOH A:880BINDING SITE FOR RESIDUE PO4 A 706
5AC5SOFTWAREGLY B:34 , ARG B:86 , HIS B:88 , ASN B:117 , ALA B:118 , SER B:222 , HOH B:718 , HOH B:798 , HOH B:816 , HOH B:834BINDING SITE FOR RESIDUE PO4 B 707
6AC6SOFTWAREGLY C:34 , SER C:35 , ARG C:86 , HIS C:88 , ASN C:117 , ALA C:118 , SER C:222 , HOH C:891 , HOH C:897BINDING SITE FOR RESIDUE PO4 C 708
7AC7SOFTWAREALA A:99 , ARG A:103 , ILE A:148 , VAL A:150 , HOH A:813BINDING SITE FOR RESIDUE DMS A 703
8AC8SOFTWAREALA B:99 , ARG B:103 , ILE B:148 , VAL B:150 , HOH B:833BINDING SITE FOR RESIDUE DMS B 704
9AC9SOFTWAREASN C:95 , ALA C:99 , ARG C:103 , ILE C:148 , VAL C:150 , GLN C:154 , HOH C:732 , HOH C:768BINDING SITE FOR RESIDUE DMS C 705

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:199 -Pro A:200
2Gly B:199 -Pro B:200
3Gly C:199 -Pro C:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TCU)

(-) 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:282
 aligned with Q9BMI9_SCHMA | Q9BMI9 from UniProtKB/TrEMBL  Length:287

    Alignment length:285
                                    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     
         Q9BMI9_SCHMA     3 ESVTANIENVKKVAHHIQKLTSIVPEIGIICGSGLGKLADGVKDKITIPYTKIPNFPQTSVVGHSGNLIFGTLSGRKVVVMQGRFHMYEGYSNDTVALPIRVMKLLGVKILMVSNAAGGLNRSLKLGDFVILKDHIYLPGLGLNNILVGPNQEAFGTRFPALSNAYDRDLRKLAVQVAEENGFGNLVHQGVYVMNGGPCYETPAECTMLLNMGCDVVGMSTIPEVVIARHCGIQVFAVSLVTNISVLDVESDLKPNHEEVLATGAQRAELMQSWFEKIIEKLPKD 287
               SCOP domains d1tcua_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1tcuA00 A:3-287  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.....eeee......hhhhhheeeeeee.hhh.......---...eeeeeee..eeeeeee...hhhhh.hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeehhhhhh........................hhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tcu A   3 ESVTANIENVKKVAHHIQKLTSIVPEIGIICGSGLGKLADGVKDKITIPYTKIPNFPQTS---HSGNLIFGTLSGRKVVVMQGRFHMYEGYSNDTVALPIRVMKLLGVKILMVSNAAGGLNRSLKLGDFVILKDHIYLPGLGLNNILVGPNQEAFGTRFPALSNAYDRDLRKLAVQVAEENGFGNLVHQGVYVMNGGPCYETPAECTMLLNMGCDVVGMSTIPEVVIARHCGIQVFAVSLVTNISVLDVESDLKPNHEEVLATGAQRAELMQSWFEKIIEKLPKD 287
                                    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     
                                                                                      62  66                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with Q9BMI9_SCHMA | Q9BMI9 from UniProtKB/TrEMBL  Length:287

    Alignment length:285
                                    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     
         Q9BMI9_SCHMA     3 ESVTANIENVKKVAHHIQKLTSIVPEIGIICGSGLGKLADGVKDKITIPYTKIPNFPQTSVVGHSGNLIFGTLSGRKVVVMQGRFHMYEGYSNDTVALPIRVMKLLGVKILMVSNAAGGLNRSLKLGDFVILKDHIYLPGLGLNNILVGPNQEAFGTRFPALSNAYDRDLRKLAVQVAEENGFGNLVHQGVYVMNGGPCYETPAECTMLLNMGCDVVGMSTIPEVVIARHCGIQVFAVSLVTNISVLDVESDLKPNHEEVLATGAQRAELMQSWFEKIIEKLPKD 287
               SCOP domains d1tcub_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1tcuB00 B:3-287  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.....eeee............eeeeeee.hhh.............eeeeeee..eeeeeee...hhhhh.hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeehhhhhh........................hhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee.......-------------..hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tcu B   3 ESVTANIENVKKVAHHIQKLTSIVPEIGIICGSGLGKLADGVKDKITIPYTKIPNFPQTSVVGHSGNLIFGTLSGRKVVVMQGRFHMYEGYSNDTVALPIRVMKLLGVKILMVSNAAGGLNRSLKLGDFVILKDHIYLPGLGLNNILVGPNQEAFGTRFPALSNAYDRDLRKLAVQVAEENGFGNLVHQGVYVMNGGPCYETPAECTMLLNMGCDVVGMSTIPEVVIARHCGIQVFAVSLVTNISVLDVES-------------AQRAELMQSWFEKIIEKLPKD 287
                                    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|        -    |  272       282     
                                                                                                                                                                                                                                                                                    253           267                    


Chain C from PDB  Type:PROTEIN  Length:285
 aligned with Q9BMI9_SCHMA | Q9BMI9 from UniProtKB/TrEMBL  Length:287

    Alignment length:285
                                    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     
         Q9BMI9_SCHMA     3 ESVTANIENVKKVAHHIQKLTSIVPEIGIICGSGLGKLADGVKDKITIPYTKIPNFPQTSVVGHSGNLIFGTLSGRKVVVMQGRFHMYEGYSNDTVALPIRVMKLLGVKILMVSNAAGGLNRSLKLGDFVILKDHIYLPGLGLNNILVGPNQEAFGTRFPALSNAYDRDLRKLAVQVAEENGFGNLVHQGVYVMNGGPCYETPAECTMLLNMGCDVVGMSTIPEVVIARHCGIQVFAVSLVTNISVLDVESDLKPNHEEVLATGAQRAELMQSWFEKIIEKLPKD 287
               SCOP domains d1tcuc_ C: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1tcuC00 C:3-287  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) -------------------------PNP_UDP_1-1tcuC01 C:28-282                                                                                                                                                                                                                                     ----- Pfam domains (1)
           Pfam domains (2) -------------------------PNP_UDP_1-1tcuC02 C:28-282                                                                                                                                                                                                                                     ----- Pfam domains (2)
           Pfam domains (3) -------------------------PNP_UDP_1-1tcuC03 C:28-282                                                                                                                                                                                                                                     ----- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhh.....eeee....hhhhhhh.eeeeeee.hhh......ee..ee.eeeeeee..eeeeeee...hhhhh.hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeehhhhh........................hhhhhhhhhhhhhhh.hhh.eeeeeeee.......hhhhhhhhhhh...eee..hhhhhhhhhhh..eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tcu C   3 ESVTANIENVKKVAHHIQKLTSIVPEIGIICGSGLGKLADGVKDKITIPYTKIPNFPQTSVVGHSGNLIFGTLSGRKVVVMQGRFHMYEGYSNDTVALPIRVMKLLGVKILMVSNAAGGLNRSLKLGDFVILKDHIYLPGLGLNNILVGPNQEAFGTRFPALSNAYDRDLRKLAVQVAEENGFGNLVHQGVYVMNGGPCYETPAECTMLLNMGCDVVGMSTIPEVVIARHCGIQVFAVSLVTNISVLDVESDLKPNHEEVLATGAQRAELMQSWFEKIIEKLPKD 287
                                    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
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: PUP (121)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q9BMI9_SCHMA | Q9BMI9)
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: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).
biological process
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9BMI9_SCHMA | Q9BMI9: 1tcv 1td1 3djf 3e0q 3e9r 3e9z 3f8w 3faz 3fb1 3fnq 3iex

(-) Related Entries Specified in the PDB File

1tcv CRYSTAL STRUCTURE OF THE PURINE NUCLEOSIDE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH NON-DETERGENT SULFOBETAINE 195 AND ACETATE
1td1 CRYSTAL STRUCTURE OF THE PURINE NUCLEOSIDE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ACETATE