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(-) Description

Title :  X-RAY STRUCTURE OF THE URIDINE PHOSPHORYLASE FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH THYMIDINE AT 2.40 A RESOLUTION
 
Authors :  S. E. Sotnichenko, A. A. Lashkov, A. G. Gabdoulkhakov, A. M. Mikhailov
Date :  16 Jan 14  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rossman Fold, Transferase, Phosphat-Ion, Pirimidine Nucleozide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Sotnichenko, A. A. Lashkov, A. G. Gabdoulkhakov, A. M. Mikhailov
X-Ray Structure Of The Uridine Phosphorylase From Salmonell Typhimurium In Complex With Thymidine At 2. 40 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
    Expression System Vector Type: PLASMID
    Gene: STM3968, STMD1.21, UDP
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720
    Synonym: UPASE, URDPASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2IPA1Ligand/IonISOPROPYL ALCOHOL
3K1Ligand/IonPOTASSIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6THM5Ligand/IonTHYMIDINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:69 , ARG A:91 , THR A:94 , GLN A:166 , MET A:197 , GLU A:198 , ILE A:220 , ARG B:48BINDING SITE FOR RESIDUE THM A 301
02AC2SOFTWAREALA C:36BINDING SITE FOR RESIDUE IPA A 302
03AC3SOFTWAREHIS A:8 , ARG A:48 , THR B:94 , PHE B:162 , GLN B:166 , ARG B:168 , TYR B:195 , GLU B:196 , GLU B:198 , VAL B:221BINDING SITE FOR RESIDUE THM B 301
04AC4SOFTWAREHIS C:101 , VAL C:153BINDING SITE FOR RESIDUE EDO C 301
05AC5SOFTWAREPHE C:7 , HIS C:8 , ARG C:48 , ILE D:69 , THR D:94 , PHE D:162 , GLN D:166 , ARG D:168 , TYR D:195 , GLU D:196 , MET D:197 , GLU D:198BINDING SITE FOR RESIDUE THM D 301
06AC6SOFTWARETHR A:233 , ASN D:230BINDING SITE FOR RESIDUE PEG D 302
07AC7SOFTWAREILE E:69 , ARG E:91 , THR E:94 , GLY E:96 , PHE E:162 , GLN E:166 , TYR E:195 , GLU E:196 , GLU E:198 , ILE E:220 , VAL E:221BINDING SITE FOR RESIDUE THM E 301
08AC8SOFTWAREHIS D:101 , VAL D:153 , PRO E:100 , VAL E:131 , ALA E:132 , ASP E:133BINDING SITE FOR RESIDUE PG4 E 302
09AC9SOFTWARELYS A:60 , ALA E:231 , GLU E:232BINDING SITE FOR RESIDUE EDO E 303
10BC1SOFTWAREHIS E:8 , PHE F:162 , GLN F:166 , ARG F:168 , TYR F:195 , GLU F:196 , MET F:197 , GLU F:198 , VAL F:221BINDING SITE FOR RESIDUE THM F 301
11BC2SOFTWAREGLU E:49 , ILE E:69 , SER E:73 , GLU F:49 , ILE F:69 , SER F:73BINDING SITE FOR RESIDUE K F 302
12BC3SOFTWAREHIS F:101 , VAL F:153BINDING SITE FOR RESIDUE EDO F 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Leu A:84 -Gly A:85
2Ala A:231 -Glu A:232
3Leu B:84 -Gly B:85
4Gln B:209 -Gly B:210
5Ala B:231 -Glu B:232
6Ser C:4 -Asp C:5
7Ala C:231 -Glu C:232
8Leu D:16 -Gln D:17
9Leu D:84 -Gly D:85
10Ala D:231 -Glu D:232
11Leu E:84 -Gly E:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OGK)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh..eee..eeeee.........eeeeeeeeee..hhhhh......ee.hhhhhhhhhhhhhhhh....eeeeeee.................hhhhhhhhhhhhh....eee.hhhhhhhhhhh...eee.eeeeeee.........hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogk A   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 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 B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eee......hhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhhh..eeeeeeeee.................hhhhhhhhhhhhhhheeeee.hhhhhhhhhhhhh.eeeeeeeeeee.............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogk B   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 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 C from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeee.....hhhhhhhhhhhhhh....eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhhh..eeeeeeeee.................hhhhhhhhhhhhhhheeeee.hhhhhhhhhhhhh.eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogk C   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh....eee......hhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeee.hhhhhh.........hhhhhhhhhhhhhhhh..eeeeeeeee.................hhhhh.hhhhhhh....eee.hhhhhhhhhhhhh.eeeeeeeeeee............hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogk D   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 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 E from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhh...eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeee..hhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeeee......................hhhhhhhhhh..eee.hhhhhhhhhhh...eeeeeeeeeee.............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogk E   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 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 F from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eeeee.hhhhhhhhh...eeeeeee......eeeeee..eeeeee....hhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee..hhhhhh.........hhhhhhhhhhhhhhhh..eeeeeeee.......................hhhhhhhhhheeeee.hhhhhhhhhhh...eeeeeeeeeee.............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ogk F   4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233||     248     
                                                                                                                                                                                                                                                                234|             
                                                                                                                                                                                                                                                                 240
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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 4OGK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gln B:209 - Gly B:210   [ RasMol ]  
    Leu A:84 - Gly A:85   [ RasMol ]  
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 Related Entries

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UniProtKB/Swiss-Prot
        UDP_SALTY | P0A1F6: 1ryz 1sj9 1y1q 1y1r 1y1s 1y1t 1zl2 2hn9 2hrd 2hsw 2hwu 2i8a 2iq5 2oec 2oxf 2pga 2qdk 2rj3 3c74 3ddo 3dps 3fwp 4e1v

(-) Related Entries Specified in the PDB File

4e1v 4ogl