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(-) Description

Title :  METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH ADENINE IN SPACE GROUP P212121
 
Authors :  J. R. Torini, R. Demarco, J. Brandao-Neto, H. M. Pereira
Date :  10 Jun 13  (Deposition) - 11 Jun 14  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
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, Phsophorylase, Nucleoside Phosphorylase, Enzyme (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 - S-METHYL-5'-THIOADENOSINE 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: SMMTAP
    Gene: SMMTAP
    Organism Common: BLOOD FLUKE
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183
    Strain: BH
    Synonym: 5'-METHYLTHIOADENOSINE PHOSPHORYLASE

 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, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1ADE6Ligand/IonADENINE
2GOL6Ligand/IonGLYCEROL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1ADE3Ligand/IonADENINE
2GOL3Ligand/IonGLYCEROL
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ADE3Ligand/IonADENINE
2GOL3Ligand/IonGLYCEROL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:88 , CYS A:89 , GLY A:90 , PHE A:187 , THR A:229 , ASP A:230 , ASP A:232 , VAL A:246 , GOL A:302 , HOH A:403BINDING SITE FOR RESIDUE ADE A 301
02AC2SOFTWARESER A:12 , ALA A:88 , PHE A:187 , MET A:206 , VAL A:246 , ADE A:301 , HOH A:406 , HOH A:429 , GLN B:289BINDING SITE FOR RESIDUE GOL A 302
03AC3SOFTWAREALA B:88 , CYS B:89 , GLY B:90 , VAL B:204 , MET B:206 , THR B:229 , ASP B:230 , ASP B:232 , VAL B:246 , GOL B:302 , HOH B:407BINDING SITE FOR RESIDUE ADE B 301
04AC4SOFTWARESER B:12 , MET B:206 , VAL B:246 , ADE B:301 , HOH B:446 , HOH B:461 , HIS C:131 , GLN C:289BINDING SITE FOR RESIDUE GOL B 302
05AC5SOFTWAREALA C:88 , CYS C:89 , GLY C:90 , ASN C:205 , THR C:229 , ASP C:230 , ASP C:232 , GOL C:302 , HOH C:407BINDING SITE FOR RESIDUE ADE C 301
06AC6SOFTWAREGLN A:289 , SER C:12 , ALA C:88 , PHE C:187 , MET C:206 , VAL C:246 , ADE C:301 , HOH C:412 , HOH C:430BINDING SITE FOR RESIDUE GOL C 302
07AC7SOFTWAREALA D:88 , CYS D:89 , GLY D:90 , VAL D:204 , THR D:229 , ASP D:230 , ASP D:232 , VAL D:246 , GOL D:302 , HOH D:402 , HOH D:407BINDING SITE FOR RESIDUE ADE D 301
08AC8SOFTWARESER D:12 , ALA D:88 , PHE D:187 , MET D:206 , VAL D:246 , ADE D:301 , HOH D:402 , HOH D:459 , GLN F:289BINDING SITE FOR RESIDUE GOL D 302
09AC9SOFTWAREGLN D:289 , SER E:12 , ALA E:88 , MET E:206 , VAL E:246 , ADE E:301 , HOH E:483BINDING SITE FOR RESIDUE GOL D 303
10BC1SOFTWAREGOL D:303 , ALA E:88 , CYS E:89 , GLY E:90 , VAL E:204 , ASN E:205 , MET E:206 , THR E:229 , ASP E:230 , ASP E:232 , HOH E:403BINDING SITE FOR RESIDUE ADE E 301
11BC2SOFTWAREHIS E:131 , GLN E:289 , SER F:12 , PHE F:187 , MET F:206 , VAL F:246 , ADE F:301 , HOH F:408 , HOH F:469BINDING SITE FOR RESIDUE GOL E 302
12BC3SOFTWAREGOL E:302 , ALA F:88 , CYS F:89 , GLY F:90 , PHE F:187 , ASN F:205 , THR F:229 , ASP F:230 , ASP F:232 , HOH F:401BINDING SITE FOR RESIDUE ADE F 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L5C)

(-) Cis Peptide Bonds  (25, 25)

Asymmetric Unit
No.Residues
1His A:170 -Pro A:171
2Gly A:184 -Pro A:185
3Val A:209 -Pro A:210
4Glu A:238 -Glu A:239
5His B:170 -Pro B:171
6Gly B:184 -Pro B:185
7Val B:209 -Pro B:210
8Glu B:238 -Glu B:239
9His C:170 -Pro C:171
10Gly C:184 -Pro C:185
11Val C:209 -Pro C:210
12Glu C:238 -Glu C:239
13His D:170 -Pro D:171
14Gly D:184 -Pro D:185
15Val D:209 -Pro D:210
16Glu D:238 -Glu D:239
17Phe E:20 -Lys E:21
18His E:170 -Pro E:171
19Gly E:184 -Pro E:185
20Val E:209 -Pro E:210
21Glu E:238 -Glu E:239
22His F:170 -Pro F:171
23Gly F:184 -Pro F:185
24Val F:209 -Pro F:210
25Glu F:238 -Glu F:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L5C)

(-) Exons   (0, 0)

(no "Exon" information available for 4L5C)

(-) 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............eeeeee..eeeeeee.............hhhhhhhhhhhhh..eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5c A   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 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.............hhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5c B   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 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:290
                                                                                                                                                                                                                                                                                                                                  
               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..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5c C   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDLL 292
                                    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       292


Chain D 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........hhhhhhhhhhhhhhhhhh..eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5c D   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 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 E from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...........eeeee............eeeeee..eeeeeee........hhhhhhhhhhhhhhhhh...eeee..eee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5c E   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDLL 292
                                    12        22        32        42        52        62        72        82   ||   93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283         
                                                                                                              86|                                                                                                                                                                                                            
                                                                                                               88                                                                                                                                                                                                            


Chain F 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.............hhhhhhhhhhhh...eeeeeeeeee.........eee..eeeee........ee.....ee...........hhhhhhhhhhhhhhh..eee.....hhhhh...eee...eeeee......hhhhhhhhhhh...eee....hhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l5c F   3 KVKVGIIGGSGFDDPNLFKKVGVRQVTTPFGKPSDTLVEGFVGDVACVVLPRHGKGHLIPPSEVNYRANVWALKDLGCTHILATNACGSLQEDLVPGDFVVLNQFMDKTWGRENTFYGSKPDSLKGVLHMPMAEPFCERTRQILIQAARNKSINVYDKKTMDKSACIHPCVHAEGSAVTINGPRFSTRCESFIHKAMGLDIVNMTLVPEVSLAREAGLSYASIAIVTDFDCWKSEEEHVCVDMVLEQFRKSVVHVREILLEAVALIGAEDWTKTIEANKALVMSSRQDL 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
   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 4L5C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L5C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L5C)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:238 - Glu A:239   [ RasMol ]  
    Glu B:238 - Glu B:239   [ RasMol ]  
    Glu C:238 - Glu C:239   [ RasMol ]  
    Glu D:238 - Glu D:239   [ RasMol ]  
    Glu E:238 - Glu E:239   [ RasMol ]  
    Glu F:238 - Glu F:239   [ RasMol ]  
    Gly A:184 - Pro A:185   [ RasMol ]  
    Gly B:184 - Pro B:185   [ RasMol ]  
    Gly C:184 - Pro C:185   [ RasMol ]  
    Gly D:184 - Pro D:185   [ RasMol ]  
    Gly E:184 - Pro E:185   [ RasMol ]  
    Gly F:184 - Pro F:185   [ RasMol ]  
    His A:170 - Pro A:171   [ RasMol ]  
    His B:170 - Pro B:171   [ RasMol ]  
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    Phe E:20 - Lys E:21   [ RasMol ]  
    Val A:209 - Pro A:210   [ RasMol ]  
    Val B:209 - Pro B:210   [ RasMol ]  
    Val C:209 - Pro C:210   [ RasMol ]  
    Val D:209 - Pro D:210   [ RasMol ]  
    Val E:209 - Pro E:210   [ RasMol ]  
    Val F:209 - Pro F:210   [ RasMol ]  
 
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 Related Entries

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

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        I0B503_SCHMA | I0B503: 4l5a 4l5y 4l6i 5f73 5f76 5f77 5f78 5f7j 5f7o 5f7x 5f7z 5fak

(-) Related Entries Specified in the PDB File

4l5a METHYLTHIOADENOSINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH TUBERCIDIN