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(-) Description

Title :  X-RAY STRUCTURE URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH THYMINE AT 1.25 A RESOLUTION
 
Authors :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date :  16 Jan 14  (Deposition) - 04 Mar 15  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rossmann Fold, Transferase, Nucleoside, Phosphate Ion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, T. Balaev, A. S. Seregina, C. Mironov, C. Betzel, A. M. Mikhailov
X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae In Complex With Thymine At 1. 25 A Resolution
Crystallogr. Rep. 2016
PubMed: search  |  Reference-DOI: 10.1134/S1063774516060134

(-) Compounds

Molecule 1 - URIDINE PHOSPHORYLASE
    Chains: A, B, C, D, E, F
    EC Number: 2.4.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMZ21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UDP, VC_1034
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric/Biological Unit (5, 25)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2GOL6Ligand/IonGLYCEROL
3NA3Ligand/IonSODIUM ION
4TDR6Ligand/IonTHYMINE
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:93 , THR A:94 , GLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , GLU A:195 , MET A:196 , ILE A:219 , ILE A:220 , GOL A:303 , HOH A:402BINDING SITE FOR RESIDUE TDR A 301
02AC2SOFTWAREARG A:178 , HOH A:408 , HOH A:409 , HOH A:603 , HOH A:674 , HOH A:721 , LEU B:120 , HOH F:626BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREGLU A:197 , TDR A:301 , HOH A:459 , HOH A:503 , HOH A:527 , HOH A:723 , HIS B:7BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWAREGLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72BINDING SITE FOR RESIDUE NA A 304
05AC5SOFTWAREGLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , GLU B:195 , MET B:196 , ILE B:220 , TRS B:303 , HOH B:418 , HOH B:732BINDING SITE FOR RESIDUE TDR B 301
06AC6SOFTWAREPHE B:6 , HIS B:7 , GLY B:9 , HIS B:46 , HOH B:711BINDING SITE FOR RESIDUE EDO B 302
07AC7SOFTWAREHIS A:7 , ARG A:47 , ILE B:68 , THR B:93 , GLU B:195 , MET B:196 , GLU B:197 , TDR B:301 , HOH B:467 , HOH B:509BINDING SITE FOR RESIDUE TRS B 303
08AC8SOFTWARETHR C:94 , GLY C:95 , PHE C:161 , GLN C:165 , ARG C:167 , PHE C:194 , GLU C:195 , MET C:196 , ILE C:220 , GOL C:305 , HOH C:408BINDING SITE FOR RESIDUE TDR C 301
09AC9SOFTWAREHOH B:724 , ARG C:178 , HOH C:414 , HOH C:417 , HOH C:643 , HOH C:649 , HOH C:683 , LEU D:120BINDING SITE FOR RESIDUE EDO C 302
10BC1SOFTWAREASP C:132 , HOH C:407 , HOH C:426 , HOH C:554 , HOH C:766BINDING SITE FOR RESIDUE EDO C 303
11BC2SOFTWARELYS C:3 , GLN C:82 , HOH C:674 , ASP D:169 , THR D:170 , PHE D:171 , HOH D:544BINDING SITE FOR RESIDUE EDO C 304
12BC3SOFTWAREPHE C:161 , GLU C:197 , TDR C:301 , HOH C:476 , HOH C:491 , HIS D:7BINDING SITE FOR RESIDUE GOL C 305
13BC4SOFTWAREGLU C:48 , ILE C:68 , SER C:72 , GLU D:48 , ILE D:68 , SER D:72BINDING SITE FOR RESIDUE NA C 306
14BC5SOFTWARETHR D:94 , GLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , GLU D:195 , MET D:196 , ILE D:220 , GOL D:302 , HOH D:409BINDING SITE FOR RESIDUE TDR D 301
15BC6SOFTWAREHIS C:7 , ARG C:47 , ILE D:68 , PHE D:161 , GLU D:197 , TDR D:301 , GOL D:303 , HOH D:452 , HOH D:468BINDING SITE FOR RESIDUE GOL D 302
16BC7SOFTWAREARG C:47 , HOH C:791 , PHE D:161 , GLU D:226 , GOL D:302BINDING SITE FOR RESIDUE GOL D 303
17BC8SOFTWAREGLY E:95 , PHE E:161 , GLN E:165 , ARG E:167 , GLU E:195 , MET E:196 , ILE E:220 , GOL E:304 , HOH E:421 , HOH E:485 , HOH E:545 , HOH E:742BINDING SITE FOR RESIDUE TDR E 301
18BC9SOFTWAREHOH C:501 , MET D:125 , MET E:125 , HOH E:744BINDING SITE FOR RESIDUE EDO E 302
19CC1SOFTWAREARG E:178 , HOH E:407 , HOH E:420 , HOH E:581 , HOH E:598 , HOH E:664 , HOH E:745 , LEU F:120BINDING SITE FOR RESIDUE EDO E 303
20CC2SOFTWAREILE E:68 , THR E:93 , PHE E:161 , MET E:196 , GLU E:197 , TDR E:301 , HOH E:453 , HOH E:655 , HIS F:7 , HOH F:646BINDING SITE FOR RESIDUE GOL E 304
21CC3SOFTWAREGLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72BINDING SITE FOR RESIDUE NA E 305
22CC4SOFTWARETHR F:93 , THR F:94 , GLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , GLU F:195 , MET F:196 , ILE F:219 , ILE F:220 , GOL F:304 , HOH F:406BINDING SITE FOR RESIDUE TDR F 301
23CC5SOFTWAREGLY F:17 , GLN F:59 , SER F:60 , HOH F:461BINDING SITE FOR RESIDUE EDO F 302
24CC6SOFTWAREMET A:125 , HOH A:461 , HOH E:493 , MET F:125BINDING SITE FOR RESIDUE EDO F 303
25CC7SOFTWAREHIS E:7 , PHE F:161 , GLU F:197 , TDR F:301 , HOH F:468 , HOH F:470 , HOH F:557BINDING SITE FOR RESIDUE GOL F 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeee....hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogl A   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPLKETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     ||236       246       
                                                                                                                                                                                                                                                           228|                    
                                                                                                                                                                                                                                                            233                    


Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeee....hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogl B   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    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 


Chain C from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeee...hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogl C   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    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 


Chain D from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeee...hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogl D   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    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 


Chain E from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeee.hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogl E   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    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 


Chain F from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh...eeee....hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogl F   2 TKTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKML 252
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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 4OGL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ogl
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  Q9KT71_VIBCH | Q9KT71
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9KT71_VIBCH | Q9KT71: 4oeh
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        Q9KT71_VIBCH | Q9KT71: 3o6v 3pns

(-) Related Entries Specified in the PDB File

4g8j 4h1t 4ogk