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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT Q289L OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH TUBERCIDIN
 
Authors :  J. R. Torini, J. Brandao-Neto, R. Demarco, H. M. Pereira
Date :  08 Dec 15  (Deposition) - 14 Dec 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Torini, J. Brandao-Neto, R. Demarco, H. D. Pereira
Crystal Structure Of Schistosoma Mansoni Adenosine Phosphorylase/5'-Methylthioadenosine Phosphorylase And Its Importance On Adenosine Salvage Pathway.
Plos Negl Trop Dis V. 10 05178 2016
PubMed-ID: 27935959  |  Reference-DOI: 10.1371/JOURNAL.PNTD.0005178

(-) Compounds

Molecule 1 - METHYLTHIOADENOSINE PHOSPHORYLASE
    Chains: A, B, C
    EC Number: 2.4.2.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ENZYME
    Mutation: YES
    Organism Common: BLOOD FLUKE
    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  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2TBN3Ligand/Ion'2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:63 , ALA A:88 , CYS A:89 , GLY A:90 , VAL A:204 , MET A:206 , THR A:229 , ASP A:230 , ASP A:232 , SO4 A:302 , HOH A:429 , HIS C:131binding site for residue TBN A 301
2AC2SOFTWAREGLY A:11 , SER A:12 , ARG A:54 , HIS A:55 , ALA A:88 , THR A:207 , TBN A:301binding site for residue SO4 A 302
3AC3SOFTWAREPRO B:63 , ALA B:88 , CYS B:89 , GLY B:90 , PHE B:187 , VAL B:204 , ASN B:205 , MET B:206 , THR B:229 , ASP B:232 , SO4 B:302 , HOH B:455 , HOH B:562 , HOH B:586binding site for residue TBN B 301
4AC4SOFTWAREGLY B:11 , SER B:12 , ARG B:54 , HIS B:55 , ALA B:88 , ASN B:205 , THR B:207 , TBN B:301 , HOH B:525binding site for residue SO4 B 302
5AC5SOFTWAREHIS B:131 , PRO C:63 , ALA C:88 , CYS C:89 , GLY C:90 , PHE C:187 , VAL C:204 , ASN C:205 , MET C:206 , THR C:229 , ASP C:232 , SO4 C:302 , HOH C:480 , HOH C:481 , HOH C:537 , HOH C:613binding site for residue TBN C 301
6AC6SOFTWAREGLY C:11 , SER C:12 , ARG C:54 , HIS C:55 , ASN C:87 , ALA C:88 , ASN C:205 , THR C:207 , TBN C:301 , HOH C:494binding site for residue SO4 C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F7X)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1His A:170 -Pro A:171
2Gly A:184 -Pro A:185
3Val A:209 -Pro A:210
4His B:170 -Pro B:171
5Gly B:184 -Pro B:185
6Val B:209 -Pro B:210
7His C:170 -Pro C:171
8Gly C:184 -Pro C:185
9Val C:209 -Pro C:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F7X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F7X)

(-) Exons   (0, 0)

(no "Exon" information available for 5F7X)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....eeeeee............eeeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeee.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7x A   3 KVKVGIIGGSGFFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRLDL 291
                                    12 ||     27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287    
                                      14|                                                                                                                                                                                                                                                                               
                                       20                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.............eee............eeeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7x B   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRLDL 291
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  ||   252       262       272       282         
                                                                                                                                                                                                                                                                  235|                                             
                                                                                                                                                                                                                                                                   246                                             


Chain C from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.............eee............eeeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7x C   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRLDLLHQ 294
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  ||   248       258       268       278       288      
                                                                                                                                                                                                                                                                  235|                                                    
                                                                                                                                                                                                                                                                   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 5F7X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F7X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F7X)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    His A:170 - Pro A:171   [ RasMol ]  
    His B:170 - Pro B:171   [ RasMol ]  
    His C:170 - Pro C:171   [ RasMol ]  
    Val A:209 - Pro A:210   [ RasMol ]  
    Val B:209 - Pro B:210   [ RasMol ]  
    Val C:209 - Pro C:210   [ RasMol ]  
 

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  I0B503_SCHMA | I0B503
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  2.4.2.28
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 Related Entries

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

UniProtKB/TrEMBL
        I0B503_SCHMA | I0B503: 4l5a 4l5c 4l5y 4l6i 5f73 5f76 5f77 5f78 5f7j 5f7o 5f7z 5fak

(-) Related Entries Specified in the PDB File

4l5a METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH TUBERCIDIN
4l5c METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENINE IN SPACE GROUP P212121
4l5y METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN APO FORM
4l6i METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENINE
5f73 CRYSTAL STRUCTURE OF MUTANT S12T OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN APO FORM
5f76 CRYSTAL STRUCTURE OF MUTANT S12T OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH METHYLTHIOADENOSINE
5f77 CRYSTAL STRUCTURE OF MUTANT S12T OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENINE
5f78 CRYSTAL STRUCTURE OF MUTANT N87T OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN APO FORM
5f7j CRYSTAL STRUCTURE OF MUTANT N87T OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENINE
5f7o CRYSTAL STRUCTURE OF MUTANT Q289L OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENINE