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(-) Description

Title :  X-RAY STRUCTURE URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH URIDINE AT 2.24 A RESOLUTION
 
Authors :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date :  25 Jun 15  (Deposition) - 20 Jul 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Transferase, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, V. V. Balaev, T. A. Seregina, A. S. Mironov, C. Betzel, A. M. 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
Crystallography Reports V. 61 954 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 Taxid: 562
    Gene: UDP, DN30_1909, VC39_02535, VC78_02550, VS27_10630, WG08_05660
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 29)

Asymmetric/Biological Unit (6, 29)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5TRS9Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6URI6Ligand/IonURIDINE

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:68 , ARG A:90 , THR A:93 , THR A:94 , GLY A:95 , GLN A:165 , ARG A:167 , GLU A:195 , MET A:196 , GLU A:197 , ILE A:220 , HOH A:434 , HOH A:450 , HOH A:467 , HIS B:7binding site for residue URI A 301
02AC2SOFTWAREASP A:132 , CYS A:205 , ALA A:206 , GLY A:209 , LEU A:210 , HOH A:401 , HOH A:406 , HOH A:410 , HOH A:422 , HOH A:425 , HOH A:428 , HOH A:436 , HOH A:474 , MET F:152 , GLY F:153binding site for residue TRS A 302
03AC3SOFTWARESER A:208 , GLY A:209 , HOH A:461 , GLN F:187 , ASP F:188binding site for residue PEG A 303
04AC4SOFTWAREGLY A:25 , ASP A:26 , ARG A:29 , ARG B:47binding site for residue CL A 304
05AC5SOFTWARETYR A:168binding site for residue CL A 305
06AC6SOFTWAREHIS A:7 , ILE B:68 , ARG B:90 , THR B:93 , THR B:94 , GLY B:95 , GLN B:165 , ARG B:167 , GLU B:195 , MET B:196 , GLU B:197 , ILE B:220 , HOH B:409 , HOH B:411 , HOH B:480binding site for residue URI B 301
07AC7SOFTWAREASP B:132 , CYS B:205 , ALA B:206 , LEU B:210 , HOH B:401 , HOH B:402 , HOH B:403 , HOH B:451 , HOH B:486 , HOH C:411 , HOH C:436binding site for residue TRS B 302
08AC8SOFTWAREGLN A:82 , THR B:170 , PHE B:171binding site for residue GOL B 303
09AC9SOFTWAREASP B:188 , HOH B:513 , SER C:208 , GLY C:209 , HOH C:502binding site for residue PEG B 304
10AD1SOFTWAREARG A:47 , GLY B:25 , ASP B:26binding site for residue CL B 305
11AD2SOFTWAREGLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72binding site for residue NA B 306
12AD3SOFTWARETHR C:93 , THR C:94 , GLY C:95 , PHE C:161 , GLN C:165 , ARG C:167 , MET C:196 , GLU C:197 , HOH C:401 , HOH C:418 , HOH C:430 , HIS D:7binding site for residue URI C 301
13AD4SOFTWAREASP C:132 , CYS C:205 , ALA C:206 , GLY C:209 , LEU C:210 , LYS C:211 , HOH C:402 , HOH C:413 , HOH C:417 , HOH C:425 , HOH C:463 , HOH C:478binding site for residue TRS C 302
14AD5SOFTWARESER B:208 , GLY B:209 , GLN C:187 , ASP C:188binding site for residue PEG C 303
15AD6SOFTWAREGLY C:25 , ASP C:26 , ARG C:29binding site for residue CL C 304
16AD7SOFTWAREHIS C:7 , ILE D:68 , THR D:93 , THR D:94 , GLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , GLU D:195 , MET D:196 , GLU D:197 , ILE D:220 , HOH D:408 , HOH D:472binding site for residue URI D 301
17AD8SOFTWAREASP D:132 , CYS D:205 , ALA D:206 , GLY D:209 , LEU D:210 , HOH D:401 , HOH D:404 , HOH D:405 , HOH D:411 , HOH D:414 , HOH D:447 , HOH E:448binding site for residue TRS D 302
18AD9SOFTWAREGLN B:31 , GLU B:35 , PRO B:40 , HOH B:417 , ASP D:38 , ASN D:39 , PRO D:40 , HOH D:432 , TRS F:302 , TRS F:304binding site for residue TRS D 303
19AE1SOFTWAREGLN D:31 , GLU D:35 , PRO D:40 , PHE D:42 , ASN F:39 , TRS F:304binding site for residue GOL D 304
20AE2SOFTWAREGLY D:25 , ASP D:26binding site for residue CL D 305
21AE3SOFTWAREILE E:68 , THR E:93 , THR E:94 , GLY E:95 , PHE E:161 , GLN E:165 , ARG E:167 , PHE E:194 , GLU E:195 , MET E:196 , GLU E:197 , ILE E:220 , HOH E:419 , HOH E:421 , HOH E:423 , HIS F:7binding site for residue URI E 301
22AE4SOFTWAREMET D:152 , GLY D:153 , HOH D:463 , ASP E:132 , CYS E:205 , ALA E:206 , GLY E:209 , LEU E:210 , HOH E:401 , HOH E:404 , HOH E:407 , HOH E:413 , HOH E:428 , HOH E:471binding site for residue TRS E 302
23AE5SOFTWAREHIS E:7 , ILE F:68 , ARG F:90 , THR F:93 , THR F:94 , GLY F:95 , GLN F:165 , ARG F:167 , PHE F:194 , GLU F:195 , MET F:196 , GLU F:197 , HOH F:436 , HOH F:467 , HOH F:488binding site for residue URI F 301
24AE6SOFTWAREASP B:38 , ASN B:39 , PRO B:40 , HOH B:421 , TRS D:303 , GLN F:31 , GLU F:35 , PRO F:40 , TRS F:304 , HOH F:413binding site for residue TRS F 302
25AE7SOFTWAREHOH A:408 , ASP F:132 , CYS F:205 , ALA F:206 , GLY F:209 , LEU F:210 , HOH F:401 , HOH F:404 , HOH F:408 , HOH F:430 , HOH F:432 , HOH F:444 , HOH F:453binding site for residue TRS F 303
26AE8SOFTWAREGLU B:35 , GLU D:35 , TRS D:303 , GOL D:304 , GLU F:35 , TRS F:302 , HOH F:463binding site for residue TRS F 304
27AE9SOFTWAREARG B:174 , ASN C:102 , LYS F:184 , ASP F:188binding site for residue GOL F 305
28AF1SOFTWAREGLY F:25 , ASP F:26 , ARG F:29binding site for residue CL F 306
29AF2SOFTWAREGLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72binding site for residue NA F 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C80)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C80)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C80)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C80)

(-) Exons   (0, 0)

(no "Exon" information available for 5C80)

(-) 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 ........hhhhhh...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
                 5c80 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...eee...hhhhhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhh....eeeeeeeee.................hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c80 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 ........hhhhhh...eeee..hhhhhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh..............hhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c80 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhhh..eee.hhhhhhhhhhh...eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c80 D   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPATLKETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     ||234       244         
                                                                                                                                                                                                                                                           228|                      
                                                                                                                                                                                                                                                            231                      


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..hhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhhh..eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c80 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...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh..............hhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c80 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
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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 5C80)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C80)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C80)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  5c80
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  Q9K4U1_VIBCL | Q9K4U1
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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 4oeh 4u2k 5efo 5epu

(-) Related Entries Specified in the PDB File

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