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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT N87T OF ADENOSINE/METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN APO FORM
 
Authors :  J. R. S. Torini, J. Brandao-Neto, R. Demarco, H. M. Pereira
Date :  07 Dec 15  (Deposition) - 21 Dec 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , SER A:12 , ARG A:54 , HIS A:55 , THR A:87 , ALA A:88 , THR A:207 , HOH A:436 , HOH A:477 , HOH A:484 , HOH A:486binding site for residue SO4 A 301
2AC2SOFTWAREGLY B:11 , SER B:12 , ARG B:54 , HIS B:55 , THR B:87 , ALA B:88 , THR B:207 , HOH B:439 , HOH B:465 , HOH B:477 , HOH B:483binding site for residue SO4 B 301
3AC3SOFTWAREGLY C:11 , SER C:12 , ARG C:54 , HIS C:55 , THR C:87 , ALA C:88 , THR C:207 , HOH C:470 , HOH C:482 , HOH C:483 , HOH C:515binding site for residue SO4 C 301
4AC4SOFTWAREGLY D:11 , SER D:12 , ARG D:54 , HIS D:55 , THR D:87 , ALA D:88 , THR D:207 , HOH D:449 , HOH D:452 , HOH D:478 , HOH D:507binding site for residue SO4 D 301
5AC5SOFTWAREGLY E:11 , SER E:12 , ARG E:54 , HIS E:55 , THR E:87 , ALA E:88 , THR E:207 , HOH E:469 , HOH E:472 , HOH E:498 , HOH E:510binding site for residue SO4 E 301
6AC6SOFTWAREGLY F:11 , SER F:12 , ARG F:54 , HIS F:55 , THR F:87 , ALA F:88 , THR F:207 , HOH F:450 , HOH F:463 , HOH F:477 , HOH F:537binding site for residue SO4 F 301

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:233 -A:242
2B:233 -B:242
3C:233 -C:242
4D:233 -D:242
5E:233 -E:242
6F:233 -F:242

(-) 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 5F78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F78)

(-) Exons   (0, 0)

(no "Exon" information available for 5F78)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.............eee............eeeee....eeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f78 A   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    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         


Chain B from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               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..eeeeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f78 B   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    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         


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..eeeeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f78 C   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   ||  244       254       264       274       284       
                                                                                                                                                                                                                                                                   236|                                                    
                                                                                                                                                                                                                                                                    239                                                    


Chain D from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhh.ee............eeeee....eeeeee........hhhhhhhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f78 D   3 KVKVGIIGGSGFDDPNLFGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 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      
                                            20|                                                                                                                                                                                                                                                                           
                                             24                                                                                                                                                                                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               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..eeeeeeeee..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f78 E   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    || 243       253       263       273       283        
                                                                                                                                                                                                                                                                    237|                                                    
                                                                                                                                                                                                                                                                     239                                                    


Chain F from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               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..eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f78 F   3 KVKVGIIGGSGFDDPNFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATTACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 291
                                    12     || 23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233||     249       259       269       279       289  
                                          18|                                                                                                                                                                                                                   234|                                                  
                                           20                                                                                                                                                                                                                    241
   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 5F78)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F78)

(-) Gene Ontology  (9, 9)

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  5f78
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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 5f7j 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