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(-) Description

Title :  STRUCTURE OF E. COLI URIDINE PHOSPHORYLASE COMPLEXED WITH 5-FLUOROURIDINE AND SULFATE
 
Authors :  W. Bu, E. C. Settembre, J. M. Sanders, T. P. Begley, S. E. Ealick
Date :  31 May 04  (Deposition) - 14 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Uridine Phosphorylase; Pyrimidine Nucleoside Phosphorylase; Uridine Salvage; 5-Fluorouridine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Bu, E. C. Settembre, J. M. Sanders, T. P. Begley, S. E. Ealick
Structures Of E. Coli Uridine Phosphorylase
To Be Published 2004
PubMed: search

(-) Compounds

Molecule 1 - URIDINE PHOSPHORYLASE
    Chains: A, B
    EC Number: 2.4.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Plasmid: PET28B
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Gene: UDP, B3831
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: URDPASE;
UPASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
15UD2Ligand/Ion5-FLUOROURIDINE
2K1Ligand/IonPOTASSIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
15UD6Ligand/Ion5-FLUOROURIDINE
2K-1Ligand/IonPOTASSIUM ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:26 , ARG A:30 , ARG A:91 , ILE A:92 , GLY A:93 , THR A:94 , 5UD A:3001 , ARG B:48BINDING SITE FOR RESIDUE SO4 A 482
2AC2SOFTWAREARG A:48 , GLY B:26 , ARG B:30 , ARG B:91 , ILE B:92 , GLY B:93 , THR B:94 , 5UD B:5002BINDING SITE FOR RESIDUE SO4 B 682
3AC3SOFTWAREGLU A:49 , ILE A:69 , SER A:73 , GLU B:49 , ILE B:69 , SER B:73BINDING SITE FOR RESIDUE K A 1001
4AC4SOFTWAREARG A:91 , THR A:94 , THR A:95 , GLY A:96 , PHE A:162 , GLN A:166 , ARG A:168 , GLU A:196 , MET A:197 , GLU A:198 , ILE A:220 , VAL A:221 , SO4 A:482 , HOH A:3032 , HOH A:3035 , PHE B:7 , HIS B:8BINDING SITE FOR RESIDUE 5UD A 3001
5AC5SOFTWAREHIS A:8 , ILE B:69 , ARG B:91 , THR B:94 , THR B:95 , GLY B:96 , PHE B:162 , GLN B:166 , ARG B:168 , GLU B:196 , MET B:197 , GLU B:198 , ILE B:220 , VAL B:221 , SO4 B:682 , HOH B:5020 , HOH B:5084BINDING SITE FOR RESIDUE 5UD B 5002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_UDP_1PS01232 Purine and other phosphorylases family 1 signature.UDP_ECOLI66-81
 		  2A:66-81
B:66-81
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PNP_UDP_1PS01232 Purine and other phosphorylases family 1 signature.UDP_ECOLI66-81
 		  6A:66-81
B:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 1TGV)

(-) 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_ECOLI | P12758 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_ECOLI     4 SDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1tgva_ A: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1tgvA00 A:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tgv A   4 SDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 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:242
 aligned with UDP_ECOLI | P12758 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_ECOLI     4 SDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1tgvb_ B: Uridine phosphorylase                                                                                                                                                                                                                           SCOP domains
               CATH domains 1tgvB00 B:4-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ----------------PNP_UDP_1-1tgvB01 B:20-253                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ----------------PNP_UDP_1-1tgvB02 B:20-253                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author ........hhhhhh...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee..hhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee...--------hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tgv B   4 SDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQ--------MKQTESHAVKIVVEAARRLL 253
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 |       -|      243       253
                                                                                                                                                                                                                                                       225      234
   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  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (UDP_ECOLI | P12758)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        UDP_ECOLI | P12758: 1k3f 1lx7 1rxc 1rxs 1rxu 1rxy 1t0u 1tgy 1u1c 1u1d 1u1e 1u1f 1u1g 3kvv

(-) Related Entries Specified in the PDB File

1k3f 1lx7 1rxc 1rxs 1rxu 1rxy 1tgw 1tgy