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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI URIDINE PHOSPHORYLASE AT 2.2 A RESOLUTION (TYPE-A NATIVE)
 
Authors :  T. T. Caradoc-Davies, S. M. Cutfield, I. L. Lamont, J. F. Cutfield
Date :  13 Apr 04  (Deposition) - 27 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Pentosyltransferase, Uridine Phosphorylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. T. Caradoc-Davies, S. M. Cutfield, I. L. Lamont, J. F. Cutfield
Crystal Structures Of Escherichia Coli Uridine Phosphorylas In Two Native And Three Complexed Forms Reveal Basis Of Substrate Specificity, Induced Conformational Changes And Influence Of Potassium
J. Mol. Biol. V. 337 337 2004
PubMed-ID: 15003451  |  Reference-DOI: 10.1016/J.JMB.2004.01.039

(-) Compounds

Molecule 1 - URIDINE PHOSPHORYLASE
    ChainsA, B
    EC Number2.4.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymURDPASE, 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1T0U)

(-) Sites  (0, 0)

(no "Site" information available for 1T0U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T0U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T0U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T0U)

(-) 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 1T0U)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:223
 aligned with UDP_ECOLI | P12758 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:251
                                    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 
            UDP_ECOLI     3 KSDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1t0ua_ A: Uridine phosphorylase                                                                                                                                                                                                                            SCOP domains
               CATH domains 1t0uA00 A:3-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...eee...hhhhhhhhhh..eeeeeeeee..eeeeeeee..eeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeeee...--------------------hhhhhhhh...eee.hhhhhhhhhhh...eeeeeeeeeee..--------hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0u A   3 KSDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTF--------------------SMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRT--------TMKQTESHAVKIVVEAARRLL 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162         -         -|      192       202       212       222 |       -|      242       252 
                                                                                                                                                                                         162                  183                                      224      233                    

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with UDP_ECOLI | P12758 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:251
                                    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 
            UDP_ECOLI     3 KSDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 253
               SCOP domains d1t0ub_ B: Uridine phosphorylase                                                                                                                                                                                                                            SCOP domains
               CATH domains 1t0uB00 B:3-253  [code=3.40.50.1580, no name defined]                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -----------------PNP_UDP_1-1t0uB01 B:20-253                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) -----------------PNP_UDP_1-1t0uB02 B:20-253                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author .........hhhhhh...eeee..hhhhhhhhhhh.eeeeeeeee..eeeeeeee..eeeeee....hhhhhhhhhhhhhhh...eeeeeeeeee.........eeeeeeeeee.hhhhhh......ee.hhhhhhhhhhhhhhh...eeeeeeeee...hhhhh.........hhhhhhhhhhhhhh....ee.hhhhhhhhhhhh..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------PNP_UDP_1       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0u B   3 KSDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVKIVVEAARRLL 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)
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    → 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

(-) 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 | P127581k3f 1lx7 1rxc 1rxs 1rxu 1rxy 1tgv 1tgy 1u1c 1u1d 1u1e 1u1f 1u1g 3kvv

(-) Related Entries Specified in the PDB File

1rxc UP 5-FLUOROURACIL RIBOSE-1-PHOSPHATE COMPLEX
1rxs UP 2'-DEOXYURIDINE PHOSPHATE COMPLEX
1rxu UP THYMIDINE PHOSPHATE COMPLEX
1rxy E. COLI URIDINE PHOSPHORYLASE: TYPE-B NATIVE