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(-) Description

Title :  CRYSTAL STRUCTURE OF URIDINE PHOSPHORYLASE FROM SCHISTOSOMA MANSONI IN COMPLEX WITH 5-FLUOROURACIL
 
Authors :  A. Marinho, J. Torini, L. Romanello, A. Cassago, R. Demarco, J. Brandao H. M. Pereira
Date :  03 Jul 14  (Deposition) - 14 Oct 15  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Uridine Phosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Da Silva Neto, J. R. Torini De Souza, L. Romanello, A. Cassago V. H. Serrao, R. Demarco, J. Brandao-Neto, R. C. Garratt, H. D. Pereira
Analysis Of Two Schistosoma Mansoni Uridine Phosphorylases Isoforms Suggests The Emergence Of A Protein With A Non-Canonical Function.
Biochimie V. 125 12 2016
PubMed-ID: 26898674  |  Reference-DOI: 10.1016/J.BIOCHI.2016.02.007

(-) Compounds

Molecule 1 - URIDINE PHOSPHORYLASE
    Chains: A, B, C, D
    EC Number: 2.4.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMP_082430
    Organism Common: BLOOD FLUKE
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2URF4Ligand/Ion5-FLUOROURACIL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2URF2Ligand/Ion5-FLUOROURACIL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2URF2Ligand/Ion5-FLUOROURACIL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:45 , GLY A:46 , ARG A:121 , GLY A:123 , THR A:124 , HOH A:490 , HOH A:576 , HOH A:620 , ARG B:77binding site for residue SO4 A 301
2AC2SOFTWARETHR A:124 , SER A:125 , GLY A:126 , PHE A:197 , GLN A:201 , ARG A:203 , MET A:231 , GLU A:232 , MET A:233 , ALA A:256 , ILE A:265 , HOH A:477 , HOH A:576binding site for residue URF A 302
3AC3SOFTWAREARG A:77 , CYS B:45 , GLY B:46 , ARG B:121 , GLY B:123 , THR B:124 , HOH B:474 , HOH B:607 , HOH B:694binding site for residue SO4 B 301
4AC4SOFTWARETHR B:124 , SER B:125 , GLY B:126 , PHE B:197 , GLN B:201 , ARG B:203 , MET B:231 , GLU B:232 , MET B:233 , ALA B:256 , ILE B:265 , HOH B:454 , HOH B:694binding site for residue URF B 302
5AC5SOFTWARECYS C:45 , GLY C:46 , ARG C:50 , ARG C:121 , GLY C:123 , THR C:124 , HOH C:465 , HOH C:478 , ARG D:77binding site for residue SO4 C 301
6AC6SOFTWARETHR C:124 , SER C:125 , GLY C:126 , PHE C:197 , GLN C:201 , ARG C:203 , MET C:231 , GLU C:232 , MET C:233 , ILE C:265 , HOH C:478 , HOH C:479binding site for residue URF C 302
7AC7SOFTWAREARG C:77 , GLY D:46 , ARG D:50 , ARG D:121 , GLY D:123 , THR D:124 , HOH D:488 , HOH D:572binding site for residue SO4 D 301
8AC8SOFTWARETHR D:124 , SER D:125 , GLY D:126 , PHE D:197 , GLN D:201 , ARG D:203 , MET D:231 , GLU D:232 , MET D:233 , ALA D:256 , ILE D:265 , HOH D:470 , HOH D:488binding site for residue URF D 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4TXN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TXN)

(-) 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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...............hhhhhhh...eeeee.hhhhhhhhhhhhhhhhh..............eeee..eeeee...hhhhhhhhhhhhhhhhhhhh....eeee..eeee.......eeeeeeee......eeeeee..eeeeee...hhhhhhhhhhhhhhh.....eeeeeeee....hhhhh.........hhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4txn A   8 VNSHLSELDEDVFHHFGFTTKSFDFKEKFGDVKFVCVCGSSGRIHNFAISMAKLAGLPVENIAGSHARFVLYKVDHILFADHGMGIPSALIMLHEVTKLLHYAGCKDVLFIRLGTSGGLGVKPGTIVLSDRCVNTKLEPYNELCILGKPVRRQTIVDLNTVNELKKLSENLSLECSVVVGGTIAANDFYEEQGRLDGSICTFSKEEKLAFLQSAYEHGIRNMEMEGTAITSHCYLTGHRAILVCVTAVNRLEGDQITISTDEFTLFAQRPGQLVGEYLKRNNGIIVR 296
                                    17        27        37        47        57      ||69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       
                                                                                   64|                                                                                                                                                                                                                                     
                                                                                    67                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...............hhhhhhh...eeeee.hhhhhhhhhhhhhhhhh..............eeee..eeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.......eeeeeeee......eeeeee..eeeeee...hhhhhhhhhhhhhh......eeeeeeee....hhhhh.........hhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4txn B   8 VNSHLSELDEDVFHHFGFTTKSFDFKEKFGDVKFVCVCGSSGRIHNFAISMAKLAGLPVENIAGSHARFVLYKVDHILFADHGMGIPSALIMLHEVTKLLHYAGCKDVLFIRLGTSGGLGVKPGTIVLSDRCVNTKLEPYNELCILGKPVRRQTIVDLNTVNELKKLSENLSLECSVVVGGTIAANDFYEEQGRLDGSICTFSKEEKLAFLQSAYEHGIRNMEMEGTAITSHCYLTGHRAILVCVTAVNRLEGDQITISTDEFTLFAQRPGQLVGEYLKRNNGIIV 295
                                    17        27        37        47        57      ||69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289      
                                                                                   64|                                                                                                                                                                                                                                    
                                                                                    67                                                                                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...............hhhhhhh...eeeee.hhhhhhhhhhhhhhhh.................eeee..eeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.......eeeeeeee......eeeeee..eeeeee...hhhhhhhhhhhhhhh.....eeeeeeee....hhhhh.........hhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4txn C   7 IVNSHLSELDEDVFHHFGFTTKSFDFKEKFGDVKFVCVCGSSGRIHNFAISMAKLAGLALPVENIAGSHARFVLYKVDHILFADHGMGIPSALIMLHEVTKLLHYAGCKDVLFIRLGTSGGLGVKPGTIVLSDRCVNTKLEPYNELCILGKPVRRQTIVDLNTVNELKKLSENLSLECSVVVGGTIAANDFYEEQGRLDGSICTFSKEEKLAFLQSAYEHGIRNMEMEGTAITSHCYLTGHRAILVCVTAVNRLEGDQITISTDEFTLFAQRPGQLVGEYLKRNNGIIVR 296
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296


Chain D from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...............hhhhhhh...eeeee.hhhhhhhhhhhhhhhh.................eeee..eeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.......eeeeeeee......eeeeee..eeeeee...hhhhhhhhhhhhhhh.....eeeeeeee....hhhhh.........hhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4txn D   7 IVNSHLSELDEDVFHHFGFTTKSFDFKEKFGDVKFVCVCGSSGRIHNFAISMAKLAGLALPVENIAGSHARFVLYKVDHILFADHGMGIPSALIMLHEVTKLLHYAGCKDVLFIRLGTSGGLGVKPGTIVLSDRCVNTKLEPYNELCILGKPVRRQTIVDLNTVNELKKLSENLSLECSVVVGGTIAANDFYEEQGRLDGSICTFSKEEKLAFLQSAYEHGIRNMEMEGTAITSHCYLTGHRAILVCVTAVNRLEGDQITISTDEFTLFAQRPGQLVGEYLKRNNGIIVR 296
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296
   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 4TXN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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        G4VGI0_SCHMA | G4VGI0: 4txh 4txj 4txl 4txm

(-) Related Entries Specified in the PDB File

4txh 4txj 4txl 4txm