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(-) Description

Title :  X-RAY STRUCTURE OF URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE COMPLEXED WITH URACIL AT 1.91 A RESOLUTION
 
Authors :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date :  13 Jan 14  (Deposition) - 04 Mar 15  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rossmann Fold, Transferase, Nucleoside (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. I. Prokofev, A. A. Lashkov, T. Balaev, A. S. Seregina, C. Mironov, A. G. Gabdoulkhakov, C. Betzel, Mikhailov
X-Ray Structures Of Uridine Phosphorylase From Vibrio Cholerae In Complexes With Uridine, Thymidine, Uracil, Thymine, And Phosphate Anion: Substrate Specificity Of Bacterial Uridine Phosphorylases.
V. 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 Strain: AM201
    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: 569B

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric/Biological Unit (6, 22)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2EOH3Ligand/IonETHANOL
3GOL7Ligand/IonGLYCEROL
4NA3Ligand/IonSODIUM ION
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6URA4Ligand/IonURACIL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:94 , GLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , GLU A:195 , MET A:196 , GOL A:302 , HOH A:409BINDING SITE FOR RESIDUE URA A 301
02AC2SOFTWARETHR A:93 , MET A:196 , GLU A:197 , URA A:301 , HOH A:475 , HOH A:548 , HIS B:7BINDING SITE FOR RESIDUE GOL A 302
03AC3SOFTWAREGLN A:31 , TYR A:52 , HOH A:431 , HOH A:603 , HOH A:630BINDING SITE FOR RESIDUE EDO A 303
04AC4SOFTWARELYS A:250 , HOH A:442BINDING SITE FOR RESIDUE EOH A 304
05AC5SOFTWARETHR B:93 , THR B:94 , GLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , PHE B:194 , GLU B:195 , MET B:196 , ILE B:220 , GOL B:302 , HOH B:411BINDING SITE FOR RESIDUE URA B 301
06AC6SOFTWAREHIS A:7 , THR B:93 , GLU B:195 , MET B:196 , GLU B:197 , URA B:301 , HOH B:445 , HOH B:514BINDING SITE FOR RESIDUE GOL B 302
07AC7SOFTWAREPHE B:133 , THR B:137 , LYS B:140 , HOH B:428 , HOH B:471 , HOH B:480 , PHE C:133 , THR C:137BINDING SITE FOR RESIDUE PEG B 303
08AC8SOFTWAREGLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72BINDING SITE FOR RESIDUE NA B 304
09AC9SOFTWAREPHE C:161 , GLU C:197 , HOH C:427 , HOH C:483 , HOH C:506 , HIS D:7BINDING SITE FOR RESIDUE GOL C 301
10BC1SOFTWARETHR B:110 , MET B:152 , PRO C:131 , ASP C:132 , PHE C:133 , EDO C:303 , HOH C:548BINDING SITE FOR RESIDUE EDO C 302
11BC2SOFTWAREASP C:132 , ALA C:206 , LEU C:210 , EDO C:302 , HOH C:413 , HOH C:449BINDING SITE FOR RESIDUE EDO C 303
12BC3SOFTWAREHIS C:7 , PHE D:161 , GLU D:195 , MET D:196 , GLU D:197 , HOH D:566BINDING SITE FOR RESIDUE GOL D 301
13BC4SOFTWAREGLU C:48 , ILE C:68 , SER C:72 , GLU D:48 , ILE D:68 , SER D:72BINDING SITE FOR RESIDUE NA D 303
14BC5SOFTWARETHR E:93 , THR E:94 , GLY E:95 , PHE E:161 , GLN E:165 , ARG E:167 , GLU E:195 , MET E:196 , ILE E:220 , GOL E:302 , HOH E:404BINDING SITE FOR RESIDUE URA E 301
15BC6SOFTWARETHR E:93 , GLU E:195 , MET E:196 , GLU E:197 , URA E:301 , HOH E:411 , HOH E:559 , HIS F:7BINDING SITE FOR RESIDUE GOL E 302
16BC7SOFTWAREHIS E:46 , ARG E:47 , ASP F:26BINDING SITE FOR RESIDUE EDO E 303
17BC8SOFTWAREGLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , GLU F:195 , GOL F:302 , HOH F:428 , HOH F:444BINDING SITE FOR RESIDUE URA F 301
18BC9SOFTWAREHIS E:7 , THR F:93 , GLU F:195 , MET F:196 , GLU F:197 , URA F:301 , HOH F:523BINDING SITE FOR RESIDUE GOL F 302
19CC1SOFTWAREASP F:132 , CYS F:205 , GLY F:209 , LEU F:210 , HOH F:414 , HOH F:423BINDING SITE FOR RESIDUE GOL F 303
20CC2SOFTWAREPHE E:6 , ARG F:167BINDING SITE FOR RESIDUE EOH F 304
21CC3SOFTWAREGLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72BINDING SITE FOR RESIDUE NA F 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OEH)

(-) 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: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
                 4oeh A   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 B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               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..........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oeh B   2 TKTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    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  


Chain C from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eee.....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
                 4oeh 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eee.....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
                 4oeh D   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEPDHATLKETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   ||  233       243       253
                                                                                                                                                                                                                                                         226|                         
                                                                                                                                                                                                                                                          228                         


Chain E from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...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
                 4oeh 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.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oeh F   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
   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 4OEH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  Q9KT71_VIBCH | Q9KT71
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 Related Entries

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

UniProtKB/TrEMBL
        Q9K4U1_VIBCL | Q9K4U1: 4g8j 4h1t 4ip0 4k6o 4lzw 4u2k 5c80 5efo 5epu
        Q9KT71_VIBCH | Q9KT71: 3o6v 3pns 4ogl

(-) Related Entries Specified in the PDB File

4g8j 4h1t