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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT N87T OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENINE
 
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 :  1.66
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
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, D, E, F
    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

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ADE4Ligand/IonADENINE
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:88 , CYS A:89 , GLY A:90 , PHE A:187 , VAL A:204 , ASN A:205 , THR A:229 , ASP A:230 , ASP A:232 , HOH A:429binding site for residue ADE A 301
2AC2SOFTWAREALA B:88 , CYS B:89 , GLY B:90 , PHE B:187 , VAL B:204 , ASN B:205 , THR B:229 , ASP B:230 , ASP B:232 , HOH B:422 , HOH B:458binding site for residue ADE B 301
3AC3SOFTWAREGLY B:11 , SER B:12 , ARG B:54 , HIS B:55 , THR B:87 , ALA B:88 , THR B:207 , HOH B:431 , HOH B:445 , HOH B:458 , HOH B:473binding site for residue PO4 B 302
4AC4SOFTWAREGLY C:11 , SER C:12 , ARG C:54 , HIS C:55 , THR C:87 , ALA C:88 , THR C:207 , HOH C:422 , HOH C:447 , HOH C:490 , HOH C:514binding site for residue PO4 C 301
5AC5SOFTWAREALA D:88 , CYS D:89 , GLY D:90 , PHE D:187 , VAL D:204 , ASN D:205 , THR D:229 , ASP D:230 , ASP D:232 , HOH D:431binding site for residue ADE D 301
6AC6SOFTWAREALA E:88 , CYS E:89 , GLY E:90 , PHE E:187 , VAL E:204 , ASN E:205 , THR E:229 , ASP E:230 , ASP E:232 , VAL E:246 , HOH E:423binding site for residue ADE E 301
7AC7SOFTWAREGLY E:11 , SER E:12 , ARG E:54 , HIS E:55 , THR E:87 , ALA E:88 , THR E:207 , HOH E:417 , HOH E:446 , HOH E:478binding site for residue PO4 E 302
8AC8SOFTWAREGLY F:11 , SER F:12 , ARG F:54 , HIS F:55 , THR F:87 , ALA F:88 , THR F:207 , HOH F:418 , HOH F:419 , HOH F:507 , HOH F:509binding site for residue PO4 F 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F7J)

(-) Cis Peptide Bonds  (18, 18)

Asymmetric 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
10His D:170 -Pro D:171
11Gly D:184 -Pro D:185
12Val D:209 -Pro D:210
13His E:170 -Pro E:171
14Gly E:184 -Pro E:185
15Val E:209 -Pro E:210
16His F:170 -Pro F:171
17Gly F:184 -Pro F:185
18Val F:209 -Pro F:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F7J)

(-) Exons   (0, 0)

(no "Exon" information available for 5F7J)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeee............eeeeee..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.............eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeee.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7j A   3 KVKVGIIGNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDLL 292
                                   |19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289   
                                  10|                                                                                                                                                                                                                                                                                  
                                   18                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               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..eeeeeeeeee.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7j B   1 MSKVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 


Chain C from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               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..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7j C   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDLLHQGSNDK 299
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       242       252       262       272       282       292       
                                                                                                                                                                                                                                                             230|                                                          
                                                                                                                                                                                                                                                              241                                                          


Chain D from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               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
                 5f7j D   3 KVKVGIIGGSGFDLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    12  ||    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      
                                       15|                                                                                                                                                                                                                                                                                
                                        19                                                                                                                                                                                                                                                                                


Chain E from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...........eeeee............eeeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee.hhhhhhhhhhhh..eeeeeeeeee.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7j E   1 MSKVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 


Chain F from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...................eeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f7j F   3 KVKVGIIGGSGFDRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDLLH 293
                                    12  ||    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 ||    250       260       270       280       290   
                                       15|                                                                                                                                                                                                             234|                                                  
                                        26                                                                                                                                                                                                              243
   Legend:   → Mismatch (orange background)
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  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 5F7J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F7J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F7J)

(-) Gene Ontology  (9, 9)

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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 5f7o 5f7x 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