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(-) Description

Title :  X-RAY STRUCTURE URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH ANTICANCER COMPOUND AT 2.13 A RESOLUTION
 
Authors :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date :  17 Jul 14  (Deposition) - 29 Jul 15  (Release) - 29 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
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, C. Betzel, A. M. Mikhailov
X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae In Complex With New Anticancer Compound At 1. 17 A Resolutio
To Be Published
PubMed: search

(-) 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, 15)

Asymmetric/Biological Unit (6, 15)
No.NameCountTypeFull Name
14WR2Ligand/Ion1-[(2R)-2,3-DIAMINOPROPYL]-5-FLUOROPYRIMIDINE-2,4(1H,3H)-DIONE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4M5F2Ligand/Ion1-[(2S)-2,3-DIAMINOPROPYL]-5-FLUOROPYRIMIDINE-2,4(1H,3H)-DIONE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:161 , GLN A:165 , HOH A:403 , HOH A:407binding site for residue EDO A 301
02AC2SOFTWAREARG A:178 , HOH A:504binding site for residue EDO A 302
03AC3SOFTWAREPHE A:171 , THR A:172 , SER B:208 , HOH C:424binding site for residue EDO B 301
04AC4SOFTWAREHIS A:7 , 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 , HOH B:401 , HOH B:411binding site for residue 4WR B 302
05AC5SOFTWAREILE C:68 , PHE C:161 , MET C:196 , HIS D:7binding site for residue EDO C 301
06AC6SOFTWAREARG C:167 , ARG C:222binding site for residue EDO C 302
07AC7SOFTWAREARG C:47 , GLY D:25 , ASP D:26 , GLY D:67 , ARG D:90 , GLU D:197 , M5F D:303binding site for residue GOL D 301
08AC8SOFTWAREPRO D:131 , ASP D:132 , GLY D:209 , LEU D:210 , LYS D:211 , ALA D:212 , HOH D:415 , HOH D:422binding site for residue PEG D 302
09AC9SOFTWAREHIS C:7 , THR D:93 , THR D:94 , GLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , PHE D:194 , GLU D:195 , MET D:196 , ILE D:219 , ILE D:220 , GOL D:301 , 4WR D:304 , HOH D:405 , HOH D:409 , HOH D:457binding site for residue M5F D 303
10AD1SOFTWAREHIS C:7 , THR D:93 , THR D:94 , GLY D:95 , GLN D:165 , ARG D:167 , PHE D:194 , GLU D:195 , MET D:196 , ILE D:219 , M5F D:303 , HOH D:405 , HOH D:409 , HOH D:457binding site for residue 4WR D 304
11AD2SOFTWAREASN A:39 , HOH E:415binding site for residue GOL E 301
12AD3SOFTWAREPRO E:24 , GLY E:25 , ASP E:26 , ARG E:29 , VAL E:91 , GLY E:92 , ARG F:47binding site for residue EDO E 302
13AD4SOFTWAREARG E:90 , VAL E:91 , GLY E:92 , GLU E:195 , VAL E:215 , ALA E:216binding site for residue EDO E 303
14AD5SOFTWAREPHE F:6 , ARG F:47 , HOH F:463binding site for residue TRS F 301
15AD6SOFTWAREHIS E:7 , THR F:93 , PHE F:161 , GLN F:165 , ARG F:167 , GLU F:195 , MET F:196 , ILE F:219 , ILE F:220 , HOH F:414 , HOH F:415 , HOH F:433 , HOH F:441binding site for residue M5F F 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U2K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U2K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U2K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U2K)

(-) Exons   (0, 0)

(no "Exon" information available for 4U2K)

(-) 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..hhhhhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhhh..eee.hhhhhhhhhhh...eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u2k A   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQATLKETEARSIKVVVEAARKMLK 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     
                                                                                                                                                                                                                                                       224|                      
                                                                                                                                                                                                                                                        231                      


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               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....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u2k B   2 TKTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQTLKETEARSIKVVVEAARKMLK 253
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  ||   238       248     
                                                                                                                                                                                                                                                        224|                     
                                                                                                                                                                                                                                                         232                     


Chain C from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee...hhhhhhhhhh..eeeeeeeee..eeeeeee....eeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u2k 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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeee..hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee..hhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u2k D   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 ||    241       251  
                                                                                                                                                                                                                                                       224|                   
                                                                                                                                                                                                                                                        234                   


Chain E from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeee.hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee...hhhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u2k E   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQHATLKETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 ||    237       247      
                                                                                                                                                                                                                                                       224|                       
                                                                                                                                                                                                                                                        230                       


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..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
                 4u2k 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)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4U2K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U2K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U2K)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5c80 5efo 5epu

(-) Related Entries Specified in the PDB File

4h1t 4k6o