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(-) Description

Title :  CRYSTAL STRUCTURE OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM TOXOPLASMA GONDII IN COMPLEX WITH IMMUCILLIN-H
 
Authors :  M. Ho, S. C. Almo, V. L. Schramm
Date :  25 Mar 10  (Deposition) - 06 Apr 11  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Pnp, Purine Nucleoside Phosphorylase, Immucillin H, Immh, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. M. Donaldson, M. B. Cassera, M. C. Ho, C. Zhan, E. F. Merino, G. B. Evans, P. C. Tyler, S. C. Almo, V. L. Schramm, K. Kim
Inhibition And Structure Of Toxoplasma Gondii Purine Nucleoside Phosphorylase.
Eukaryot Cell V. 13 572 2014
PubMed-ID: 24585883  |  Reference-DOI: 10.1128/EC.00308-13

(-) Compounds

Molecule 1 - PURINE NUCLEOSIDE PHOSPHORYLASE
    ChainsA, B
    EC Number2.4.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRCHIS2-TOPO
    Expression System StrainBL21-CODON PLUS (DE3)-RIPL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePNP
    Organism ScientificTOXOPLASMA GONDII
    Organism Taxid5811

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (3x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2IMH2Ligand/Ion1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2IMH6Ligand/Ion1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL
3PO46Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:71 , ARG A:93 , THR A:96 , CYS A:97 , GLY A:98 , ASP A:186 , MET A:187 , GLU A:188 , ASP A:210 , PRO A:213 , TRP A:216 , PO4 A:281 , HOH A:295 , HOH A:312 , HOH A:313 , HIS B:12 , GOL B:283BINDING SITE FOR RESIDUE IMH A 280
2AC2SOFTWAREGLY A:28 , ARG A:32 , ARG A:93 , GLY A:95 , THR A:96 , IMH A:280 , ARG B:50BINDING SITE FOR RESIDUE PO4 A 281
3AC3SOFTWAREARG A:14 , ARG A:16 , ASP A:19 , LEU A:46 , HOH A:319BINDING SITE FOR RESIDUE GOL A 282
4AC4SOFTWAREPRO A:11 , ARG A:14 , ASN A:49 , ARG A:50 , HOH A:360 , TYR B:221 , ALA B:223 , IMH B:280 , HOH B:321BINDING SITE FOR RESIDUE GOL A 283
5AC5SOFTWAREHIS A:12 , GOL A:283 , ILE B:71 , ARG B:93 , THR B:96 , CYS B:97 , GLY B:98 , PHE B:165 , ASP B:186 , MET B:187 , GLU B:188 , ASP B:210 , PRO B:213 , TRP B:216 , PO4 B:281 , HOH B:289 , HOH B:305 , HOH B:318BINDING SITE FOR RESIDUE IMH B 280
6AC6SOFTWAREARG A:50 , GLY B:28 , ARG B:32 , ARG B:93 , GLY B:95 , THR B:96 , IMH B:280BINDING SITE FOR RESIDUE PO4 B 281
7AC7SOFTWAREARG B:14 , ARG B:16 , ASP B:19 , LEU B:46 , HOH B:297BINDING SITE FOR RESIDUE GOL B 282
8AC8SOFTWARETYR A:221 , ALA A:223 , IMH A:280 , HOH A:333 , PRO B:11 , ARG B:14 , ASN B:49 , ARG B:50 , HOH B:322BINDING SITE FOR RESIDUE GOL B 283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MB8)

(-) Exons   (0, 0)

(no "Exon" information available for 3MB8)

(-) 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:248
 aligned with Q2HXR2_TOXGO | Q2HXR2 from UniProtKB/TrEMBL  Length:247

    Alignment length:248
                             1                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
         Q2HXR2_TOXGO     - -MQGMEVQPHIRLRKEDVEPVVIIVGDPARTEEVANMCEKKQELAYNREYRSFRVVYDSQPITVISHGIGCPGTSIAIEELAYLGAKVIIRAGTCGSLKPKTLKQGDVCVTYAAVNETGLISNILPEGFPCVATPHVYQALMDAAKELGIEAASGIGVTQDYFYQNGILPSKLEMYSKCCDVIDMEMSGVLGLCQARGIATCGILAVDGSPLQWDEGDYDATGVKATTGKENMIKITLKACANLRRQY 247
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhh..eeeee.hhhhhhhhhh...eeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee..........eeeeeeeee.hhhhhhhh.....ee.hhhhhhhhhhhhhhhh...eeeeeee............hhhhhhh...eee.hhhhhhhhhhhh..eeeeeeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mb8 A   3 LMQGMEVQPHIRLRKEDVEPVVIIVGDPARTEEVANMCEKKQELAYNREYRSFRVVYDSQPITVISHGIGCPGTSIAIEELAYLGAKVIIRAGTCGSLKPKTLKQGDVCVTYAAVNETGLISNILPEGFPCVATPHVYQALMDAAKELGIEAASGIGVTQDYFYQNGILPSKLEMYSKCCDVIDMEMSGVLGLCQARGIATCGILAVDGSPLQWDEGDYDATGVKATTGKENMVKITLKACANLRRQY 250
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242        

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with Q2HXR2_TOXGO | Q2HXR2 from UniProtKB/TrEMBL  Length:247

    Alignment length:248
                             1                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
         Q2HXR2_TOXGO     - -MQGMEVQPHIRLRKEDVEPVVIIVGDPARTEEVANMCEKKQELAYNREYRSFRVVYDSQPITVISHGIGCPGTSIAIEELAYLGAKVIIRAGTCGSLKPKTLKQGDVCVTYAAVNETGLISNILPEGFPCVATPHVYQALMDAAKELGIEAASGIGVTQDYFYQNGILPSKLEMYSKCCDVIDMEMSGVLGLCQARGIATCGILAVDGSPLQWDEGDYDATGVKATTGKENMIKITLKACANLRRQY 247
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------PNP_UDP_1-3mb8B01 B:22-244                                                                                                                                                                                                     ------ Pfam domains (1)
           Pfam domains (2) -------------------PNP_UDP_1-3mb8B02 B:22-244                                                                                                                                                                                                     ------ Pfam domains (2)
         Sec.struct. author .............hhhhh..eeeee.hhhhhhhhhh...eeeeeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeee..........eeeeeeeee.hhhhhhhh.....ee.hhhhhhhhhhhhhhhh...eeeeeee............hhhhhh....eee.hhhhhhhhhhhh..eeeeeeeeeehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mb8 B   3 LMQGMEVQPHIRLRKEDVEPVVIIVGDPARTEEVANMCEKKQELAYNREYRSFRVVYDSQPITVISHGIGCPGTSIAIEELAYLGAKVIIRAGTCGSLKPKTLKQGDVCVTYAAVNETGLISNILPEGFPCVATPHVYQALMDAAKELGIEAASGIGVTQDYFYQNGILPSKLEMYSKCCDVIDMEMSGVLGLCQARGIATCGILAVDGSPLQWDEGDYDATGVKATTGKENMVKITLKACANLRRQY 250
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242        

   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 3MB8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MB8)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PUP (121)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q2HXR2_TOXGO | Q2HXR2)
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: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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