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(-) Description

Title :  X-RAY STRUCTURE URIDINE PHOSPHORYLASE FROM VIBRIO CHOLERAE IN COMPLEX WITH CYTIDINE AND CYTOSINE AT 1.63A.
 
Authors :  I. I. Prokofev, A. A. Lashkov, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikh
Date :  24 Oct 15  (Deposition) - 09 Nov 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
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 Uridine At 2. 24 A Resolution
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, UDP_1, DN30_1909, EN12_05055, ERS013138_02408, ERS013140_00580, ERS013186_00327, ERS013199_00063, ERS013201_00032, ERS013202_00369, ERS013206_00377
    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, 20)

Asymmetric/Biological Unit (7, 20)
No.NameCountTypeFull Name
1CTN2Ligand/Ion4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
2CYT6Ligand/Ion6-AMINOPYRIMIDIN-2(1H)-ONE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4GOL4Ligand/IonGLYCEROL
5NA3Ligand/IonSODIUM ION
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
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
02AC2SOFTWAREGLY A:95 , PHE A:161 , GLN A:165 , ARG A:167 , GLU A:195 , MET A:196 , TRS A:303 , HOH A:413 , HOH A:492binding site for residue CYT A 302
03AC3SOFTWAREILE A:68 , GLU A:195 , MET A:196 , GLU A:197 , CYT A:302 , HOH A:418 , HOH A:424 , HOH A:497 , HIS B:7 , ARG B:47binding site for residue TRS A 303
04AC4SOFTWAREHIS A:7 , THR B:93 , PHE B:161 , GLU B:195 , MET B:196 , GLU B:197 , CYT B:302 , HOH B:416 , HOH B:482binding site for residue GOL B 301
05AC5SOFTWARETHR B:94 , GLY B:95 , PHE B:161 , GLN B:165 , ARG B:167 , GLU B:195 , MET B:196 , GOL B:301 , HOH B:445binding site for residue CYT B 302
06AC6SOFTWAREILE C:68 , GLU C:195 , MET C:196 , GLU C:197 , CYT C:303 , HOH C:449 , HOH C:455 , HIS D:7binding site for residue GOL C 301
07AC7SOFTWAREGLN C:98 , GLN C:187 , ASP C:188 , HOH C:414 , HOH C:459binding site for residue PEG C 302
08AC8SOFTWAREPHE C:161 , GLN C:165 , ARG C:167 , GLU C:195 , MET C:196 , ARG C:222 , GOL C:301 , HOH C:401 , HOH C:402 , HOH C:407binding site for residue CYT C 303
09AC9SOFTWAREGLU B:126 , ARG C:178 , PHE C:179 , SER C:182 , GLU C:185 , TRP C:186 , HOH C:425 , HOH C:542binding site for residue CYT C 304
10AD1SOFTWAREGLU C:48 , ILE C:68 , SER C:72 , GLU D:48 , ILE D:68 , SER D:72binding site for residue NA C 305
11AD2SOFTWAREARG D:167 , TYR D:168 , ASP D:169 , HOH D:415 , HOH D:427binding site for residue EDO D 301
12AD3SOFTWAREGLY D:95 , PHE D:161 , GLN D:165 , ARG D:167 , GLU D:195 , MET D:196 , ILE D:220 , GOL D:304 , HOH D:430binding site for residue CYT D 302
13AD4SOFTWAREARG D:178 , PHE D:179 , GLU D:185 , TRP D:186 , HOH D:402 , HOH D:406 , HOH D:482 , HOH D:578 , GLU E:126 , ARG F:177binding site for residue CYT D 303
14AD5SOFTWAREHIS C:7 , ILE D:68 , GLU D:195 , MET D:196 , GLU D:197 , CYT D:302 , HOH D:458 , HOH D:522binding site for residue GOL D 304
15AD6SOFTWAREGLU E:48 , ILE E:68 , SER E:72 , GLU F:48 , ILE F:68 , SER F:72binding site for residue NA E 301
16AD7SOFTWAREPRO E:24 , GLY E:25 , ASP E:26 , ARG E:29 , ARG E:90 , VAL E:91 , GLY E:92 , THR E:93 , CTN E:303 , HOH E:412 , HOH E:512 , ARG F:47binding site for residue GOL E 302
17AD8SOFTWARETHR 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 , GOL E:302 , HOH E:412 , HOH E:476 , HOH E:496 , HOH E:512 , HIS F:7binding site for residue CTN E 303
18AD9SOFTWAREPHE E:6 , ARG F:167 , ASP F:169binding site for residue EDO F 301
19AE1SOFTWAREHOH A:415 , LEU E:120 , ARG F:178 , HOH F:401 , HOH F:428 , HOH F:439 , HOH F:593binding site for residue EDO F 302
20AE2SOFTWAREHIS E:7 , THR F:93 , THR F:94 , GLY F:95 , PHE F:161 , GLN F:165 , ARG F:167 , GLU F:195 , MET F:196 , GLU F:197 , ILE F:220 , HOH F:409 , HOH F:521 , HOH F:537binding site for residue CTN F 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EFO)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               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
                 5efo A   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQPDHATLKETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 ||    235       245        
                                                                                                                                                                                                                                                       224|                         
                                                                                                                                                                                                                                                        228                         


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               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
                 5efo B   1 MTKTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   


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..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
                 5efo 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...eeee..hhhhhhhhhh..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
                 5efo 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..........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5efo E   3 KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVYRAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVNVGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHMGVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLLTMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKMLK 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252 


Chain F from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeee....hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5efo 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 5EFO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  5efo
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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 5c80 5epu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5EFO)