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(-) Description

Title :  CRYSTAL STRUCTURE OF THE URIDINE PHOSPHORYLASE FROM SALMONELLA TYPHIMURIUM AT 1.77A RESOLUTION
 
Authors :  A. G. Gabdoulkhakov, M. V. Dontsova, G. S. Kachalova, C. Betzel, S. E. Ea A. M. Mikhailov
Date :  19 Nov 04  (Deposition) - 22 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,F
Biol. Unit 1:  A,F  (3x)
Keywords :  Nucleoside Phosphorylase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Gabdoulkhakov, M. V. Dontsova, G. S. Kachalova, C. Betzel, S. E. Ealick, A. M. Mikhailov
Crystal Structures Of Salmonella Typhimurium Uridine Phosphorylase In Native And Three Complexes Forms - With Uridine, Uracil And Sulfate.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URIDINE PHOSPHORYLASE
    Chains: A, F
    EC Number: 2.4.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PBLUESCRIPT IISK
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: UDP
    Organism Scientific: SALMONELLA TYPHIMURIUM LT2
    Organism Taxid: 99287
    Strain: LT2
    Synonym: URDPASE, UPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AF
Biological Unit 1 (3x): AF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:1069 , PHE A:1162 , HOH A:3053 , HOH A:3100 , HIS F:2008 , ARG F:2048 , HOH F:3236BINDING SITE FOR RESIDUE SO4 F 4001
2AC2SOFTWARETYR A:1172 , SER A:1173 , ALA A:1189 , HOH A:3226 , GLN F:2209BINDING SITE FOR RESIDUE GOL A 5001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y1T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y1T)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_UDP_1PS01232 Purine and other phosphorylases family 1 signature.UDP_SALTY66-81
 		  2A:1066-1081
F:2066-2081
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_UDP_1PS01232 Purine and other phosphorylases family 1 signature.UDP_SALTY66-81
 		  6A:1066-1081
F:2066-2081

(-) Exons   (0, 0)

(no "Exon" information available for 1Y1T)

(-) Sequences/Alignments

Asymmetric 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
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    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
           UDP_SALTY      4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL  253
               SCOP domains d1y1ta_ A: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1y1tA00 A:1004-1253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y1t A 1004 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 1253
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253


Chain F from PDB  Type:PROTEIN  Length:218
 aligned with UDP_SALTY | P0A1F6 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:250
                                    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
           UDP_SALTY      4 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRRFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL  253
               SCOP domains d1y1tf_ F: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1y1tF00 F:2004-2253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ----------------PNP_UDP_1-1y1tF01 F:2020-2253                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) ----------------PNP_UDP_1-1y1tF02 F:2020-2253                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee...hhhhhhhhhhhhhhhh...eeeeeeeee..........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeeee...--------------------.hhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeee.------------hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y1t F 2004 SDVFHLGLTKNDLQGAQLAIVPGDPERVEKIAALMDKPVKLASHREFTSWRAELDGKAVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPMEFPAVADFACTTALVEAAKSIGATTHVGVTASSDTF--------------------SMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVN------------KQTESHAVKIVVEAARRLL 2253
                                  2013      2023      2033      2043      2053      2063      2073      2083      2093      2103      2113      2123      2133      2143      2153        |-         -      2183      2193      2203      2213        |-         - |    2243      2253
                                                                                                                                                                                       2162                 2183                                   2222         2235
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PUP (121)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,F   (UDP_SALTY | P0A1F6)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
    GO:0004850    uridine phosphorylase activity    Catalysis of the reaction: uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
biological process
    GO:0044206    UMP salvage    Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0009166    nucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

(-) Related Entries Specified in the PDB File

1ryz URIDINE PHOSPHORYLASE FROM SALMONELLA TYPHIMURIUM CRYSTAL STRUCTURE AT 2.9 A RESOLUTION
1sj9 CRYSTAL STRUCTURE OF THE URIDINE PHOSPHORYLASE FROM SALMONELLA TYPHIMURIUM AT 2.5A RESOLUTION
1y1q
1y1r
1y1s