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(-) Description

Title :  X-RAY STRUCTURE URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH THYMIDINE AT 1.29 A RESOLUTION
 
Authors :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date :  01 Aug 13  (Deposition) - 31 Dec 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, Cytoplasmic (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 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
    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, 33)

Asymmetric/Biological Unit (6, 33)
No.NameCountTypeFull Name
1CL8Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3EOH7Ligand/IonETHANOL
4MG7Ligand/IonMAGNESIUM ION
5NA3Ligand/IonSODIUM ION
6THM6Ligand/IonTHYMIDINE

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:93 , GLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , PHE A:194 , GLU A:195 , MET A:196 , GLU A:197 , ILE A:219 , HOH A:476 , HOH A:681 , HIS B:7 , ARG B:47BINDING SITE FOR RESIDUE THM A 301
02AC2SOFTWAREARG A:178 , HOH A:601 , HOH A:676 , LEU B:120 , HOH B:425 , HOH B:715 , HOH F:616BINDING SITE FOR RESIDUE EOH A 302
03AC3SOFTWAREMET A:125 , GLU A:126 , HOH A:505 , MET F:125BINDING SITE FOR RESIDUE EOH A 303
04AC4SOFTWAREGLY A:25 , ASP A:26 , ARG A:29 , HOH A:493BINDING SITE FOR RESIDUE CL A 304
05AC5SOFTWAREGLU A:48 , ILE A:68 , SER A:72 , GLU B:48 , ILE B:68 , SER B:72BINDING SITE FOR RESIDUE NA A 305
06AC6SOFTWAREASN A:221BINDING SITE FOR RESIDUE CL A 306
07AC7SOFTWAREGLN A:180 , HOH A:513 , HOH A:562 , HOH A:621 , HOH A:688 , HOH C:656BINDING SITE FOR RESIDUE MG A 307
08AC8SOFTWAREHIS A:7 , ARG A:47 , HOH A:516 , THR B:93 , GLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , PHE B:194 , GLU B:195 , MET B:196 , ILE B:220 , HOH B:426 , HOH B:442BINDING SITE FOR RESIDUE THM B 301
09AC9SOFTWAREMET B:125 , GLU C:126BINDING SITE FOR RESIDUE EOH B 302
10BC1SOFTWARELEU A:120 , HOH A:417 , HOH A:421 , ARG B:178 , HOH B:539 , HOH B:716BINDING SITE FOR RESIDUE EOH B 303
11BC2SOFTWAREGLY B:25 , ASP B:26 , ARG B:29 , HOH B:459BINDING SITE FOR RESIDUE CL B 304
12BC3SOFTWAREGLN B:180 , HOH B:454 , HOH B:503 , HOH B:524 , HOH B:559BINDING SITE FOR RESIDUE MG B 305
13BC4SOFTWARETHR C:93 , GLY C:95 , PHE C:161 , GLN C:165 , ARG C:167 , PHE C:194 , GLU C:195 , MET C:196 , GLU C:197 , ILE C:220 , HOH C:410 , HOH C:494 , HOH C:591 , HIS D:7 , ARG D:47BINDING SITE FOR RESIDUE THM C 301
14BC5SOFTWAREHOH B:677 , ARG C:178 , HOH C:429 , HOH C:433 , HOH C:757 , HOH C:758 , LEU D:120BINDING SITE FOR RESIDUE EDO C 302
15BC6SOFTWAREGLY C:25 , ASP C:26 , ARG C:29 , HOH C:480BINDING SITE FOR RESIDUE CL C 303
16BC7SOFTWAREGLU C:48 , ILE C:68 , SER C:72 , GLU D:48 , ILE D:68 , SER D:72BINDING SITE FOR RESIDUE NA C 304
17BC8SOFTWAREMG C:306 , HOH C:486 , HOH C:492 , HOH C:561 , HOH C:660BINDING SITE FOR RESIDUE MG C 305
18BC9SOFTWAREASN C:102 , MG C:305 , HOH C:486 , HOH C:488 , HOH C:492BINDING SITE FOR RESIDUE MG C 306
19CC1SOFTWAREHIS C:7 , ARG C:47 , ILE D:68 , THR D:93 , GLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , PHE D:194 , GLU D:195 , MET D:196 , GLU D:197 , ILE D:220 , HOH D:407 , HOH D:445 , HOH D:456 , HOH D:569BINDING SITE FOR RESIDUE THM D 301
20CC2SOFTWARELEU C:120 , HOH C:437 , HOH C:761 , ARG D:178 , HOH D:697BINDING SITE FOR RESIDUE EOH D 302
21CC3SOFTWAREHOH C:590 , GLY D:25 , ASP D:26 , ARG D:29 , HOH D:466BINDING SITE FOR RESIDUE CL D 303
22CC4SOFTWAREMG D:305 , HOH D:470 , HOH D:528 , HOH D:568BINDING SITE FOR RESIDUE MG D 304
23CC5SOFTWAREASN D:102 , MG D:304 , HOH D:470 , HOH D:528 , HOH D:666BINDING SITE FOR RESIDUE MG D 305
24CC6SOFTWARETHR E:93 , GLY E:95 , PHE E:161 , GLN E:165 , ARG E:167 , PHE E:194 , GLU E:195 , MET E:196 , GLU E:197 , HOH E:432 , HOH E:448 , HIS F:7 , ARG F:47BINDING SITE FOR RESIDUE THM E 301
25CC7SOFTWAREMET E:183 , GLN E:187 , HOH E:430 , HOH E:599 , HOH E:635BINDING SITE FOR RESIDUE EDO E 302
26CC8SOFTWAREARG E:178 , HOH E:676 , HOH E:684 , HOH E:706 , LEU F:120 , HOH F:416 , HOH F:422BINDING SITE FOR RESIDUE EOH E 303
27CC9SOFTWAREGLY E:25 , ASP E:26 , ARG E:29 , HOH E:493 , HOH F:488BINDING SITE FOR RESIDUE CL E 304
28DC1SOFTWAREGLN E:180 , HOH E:468 , HOH E:562 , HOH E:574 , HOH E:619 , HOH E:622BINDING SITE FOR RESIDUE MG E 305
29DC2SOFTWAREHIS E:7 , ARG E:47 , THR F:93 , GLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , PHE F:194 , GLU F:195 , MET F:196 , GLU F:197 , ILE F:219 , ILE F:220 , HOH F:480 , HOH F:611BINDING SITE FOR RESIDUE THM F 301
30DC3SOFTWAREHOH A:600 , LEU E:120 , HOH E:421 , HOH E:423 , ARG F:178 , HOH F:598 , HOH F:685BINDING SITE FOR RESIDUE EOH F 302
31DC4SOFTWAREGLY F:25 , ASP F:26 , ARG F:29 , HOH F:585 , HOH F:686BINDING SITE FOR RESIDUE CL F 303
32DC5SOFTWAREGLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72BINDING SITE FOR RESIDUE NA F 304
33DC6SOFTWAREASN F:221 , LYS F:225 , HOH F:569BINDING SITE FOR RESIDUE CL F 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LZW)

(-) 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:245
                                                                                                                                                                                                                                                                                     
               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........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lzw A   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     ||238       248     
                                                                                                                                                                                                                                                           228|                  
                                                                                                                                                                                                                                                            235                  


Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               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
                 4lzw 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...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
                 4lzw 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...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
                 4lzw 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...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
                 4lzw 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:245
                                                                                                                                                                                                                                                                                     
               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........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lzw F   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     ||238       248     
                                                                                                                                                                                                                                                           228|                  
                                                                                                                                                                                                                                                            235
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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 4LZW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  4lzw
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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 4oeh 4u2k 5c80 5efo 5epu

(-) Related Entries Specified in the PDB File

4g8j