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(-) Description

Title :  X-RAY STRUCTURE OF THE COMPLEX URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE WITH PHOSPHATE ION AT 1.29 A RESOLUTION
 
Authors :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date :  09 Jan 13  (Deposition) - 13 Aug 14  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.29
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rossmann Fold, Transferase, Phosphorylation, Nucleoside (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 Plasmid: PMZ21
    Expression System Strain: AM201
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UDP
    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  (7, 23)

Asymmetric/Biological Unit (7, 23)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3EOH1Ligand/IonETHANOL
4K1Ligand/IonPOTASSIUM ION
5NA2Ligand/IonSODIUM ION
6PO45Ligand/IonPHOSPHATE ION
7SO45Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72BINDING SITE FOR RESIDUE NA A 301
02AC2SOFTWAREHOH A:578 , HOH A:670 , HOH A:747 , GLN C:31BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREARG B:86 , HOH B:516BINDING SITE FOR RESIDUE PO4 B 301
04AC4SOFTWAREARG A:47 , GLY B:25 , ARG B:29 , ARG B:90 , VAL B:91 , GLY B:92 , THR B:93 , HOH B:439 , HOH B:489BINDING SITE FOR RESIDUE PO4 B 302
05AC5SOFTWARELYS B:140 , GLN B:144 , HOH B:604 , HOH B:626 , HOH B:655BINDING SITE FOR RESIDUE SO4 B 303
06AC6SOFTWAREARG B:177 , HOH B:457 , HOH B:505 , ARG D:177 , ARG F:177BINDING SITE FOR RESIDUE SO4 B 304
07AC7SOFTWAREGLY A:92 , THR A:93 , HOH A:550 , HOH A:564 , ARG B:47 , HOH B:634BINDING SITE FOR RESIDUE EDO B 305
08AC8SOFTWAREHOH B:413 , HOH B:437 , HOH B:438BINDING SITE FOR RESIDUE EOH B 306
09AC9SOFTWAREGLY C:25 , ARG C:29 , ARG C:90 , VAL C:91 , GLY C:92 , THR C:93 , HOH C:442 , HOH C:573 , HOH C:581 , ARG D:47BINDING SITE FOR RESIDUE PO4 C 301
10BC1SOFTWAREGLY C:95 , ARG C:167 , ILE C:220 , EDO C:303BINDING SITE FOR RESIDUE CL C 302
11BC2SOFTWARETHR C:94 , GLY C:95 , PHE C:161 , GLN C:165 , PHE C:194 , GLU C:195 , MET C:196 , CL C:302 , HOH C:524 , HOH C:573 , HOH C:579 , HOH C:580BINDING SITE FOR RESIDUE EDO C 303
12BC3SOFTWAREARG C:239 , LYS C:242 , HOH C:703BINDING SITE FOR RESIDUE EDO C 304
13BC4SOFTWAREGLU C:48 , ILE C:68 , SER C:72 , GLU D:48 , ILE D:68 , SER D:72BINDING SITE FOR RESIDUE K D 301
14BC5SOFTWAREHOH C:458 , HOH C:517 , HIS D:46 , HOH D:443 , HOH D:533 , HOH D:586 , HOH D:676BINDING SITE FOR RESIDUE SO4 D 302
15BC6SOFTWAREGLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72BINDING SITE FOR RESIDUE NA E 301
16BC7SOFTWAREARG E:90 , GLY E:92 , THR E:93 , HOH E:441 , HOH E:581 , HOH E:627 , HOH E:731 , ARG F:47BINDING SITE FOR RESIDUE SO4 E 302
17BC8SOFTWAREARG E:86 , HOH E:663 , HOH E:687BINDING SITE FOR RESIDUE SO4 E 303
18BC9SOFTWAREGLU E:166 , MET E:183 , ARG E:222 , HOH E:693 , HOH E:706BINDING SITE FOR RESIDUE EDO E 304
19CC1SOFTWAREARG E:47 , GLY F:25 , ARG F:29 , ARG F:90 , VAL F:91 , GLY F:92 , THR F:93 , HOH F:467 , HOH F:575 , HOH F:585BINDING SITE FOR RESIDUE PO4 F 301
20CC2SOFTWARELYS F:140 , GLN F:144 , HOH F:520 , HOH F:523 , HOH F:527 , HOH F:588 , HOH F:643 , HOH F:658BINDING SITE FOR RESIDUE PO4 F 302
21CC3SOFTWAREGLY F:95 , ARG F:167 , ILE F:220 , EDO F:304BINDING SITE FOR RESIDUE CL F 303
22CC4SOFTWARETHR F:94 , GLY F:95 , GLN F:165 , PHE F:194 , GLU F:195 , MET F:196 , CL F:303 , HOH F:575 , HOH F:577 , HOH F:578 , HOH F:579 , HOH F:585BINDING SITE FOR RESIDUE EDO F 304
23CC5SOFTWARESER A:207 , SER A:208 , GLY A:209 , ARG B:174 , ASP F:188 , MET F:189 , GLY F:190 , HOH F:425 , HOH F:716BINDING SITE FOR RESIDUE EDO F 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IP0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IP0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IP0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IP0)

(-) Exons   (0, 0)

(no "Exon" information available for 4IP0)

(-) 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...eeee....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
                 4ip0 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: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..........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ip0 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:250
                                                                                                                                                                                                                                                                                          
               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..........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ip0 C   4 TVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253


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
                 4ip0 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...eeee..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
                 4ip0 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...eeeee...hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ip0 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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  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 4IP0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IP0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IP0)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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

UniProtKB/TrEMBL
        Q9K4U1_VIBCL | Q9K4U1: 4g8j 4h1t 4k6o 4lzw 4oeh 4u2k 5c80 5efo 5epu

(-) Related Entries Specified in the PDB File

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