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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS CALDOLYTICUS URACIL PHOSPHORIBOSYLTRANSFERASE WITH BOUND UMP
 
Authors :  A. Kadziola, J. Neuhard, S. Larsen
Date :  27 Feb 01  (Deposition) - 05 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Uracil Phosphoribosyltransferase, Salvage Pathway, Bacillus Caldolyticus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Kadziola, J. Neuhard, S. Larsen
Structure Of Product-Bound Bacillus Caldolyticus Uracil Phosphoribosyltransferase Confirms Ordered Sequential Substrate Binding.
Acta Crystallogr. , Sect. D V. 58 936 2002
PubMed-ID: 12037295  |  Reference-DOI: 10.1107/S0907444902005024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL PHOSPHORIBOSYLTRANSFERASE
    ChainsA, B
    EC Number2.4.2.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneUPP
    Organism ScientificBACILLUS CALDOLYTICUS
    Organism Taxid1394
    SynonymUMP PYROPHOSPHORYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1U5P2Ligand/IonURIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:131 , MET A:133 , ALA A:135 , THR A:136 , GLY A:137 , GLY A:138 , SER A:139 , GLY A:192 , TYR A:193 , ILE A:194 , GLY A:199 , ASP A:200 , ALA A:201 , HOH A:251BINDING SITE FOR RESIDUE U5P A 250
2AC2SOFTWAREASP B:131 , MET B:133 , ALA B:135 , THR B:136 , GLY B:137 , GLY B:138 , SER B:139 , GLY B:192 , TYR B:193 , ILE B:194 , GLY B:199 , ASP B:200 , ALA B:201 , HOH B:252BINDING SITE FOR RESIDUE U5P B 260

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I5E)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:78 -Arg A:79
2Val A:195 -Pro A:196
3Leu B:78 -Arg B:79
4Val B:195 -Pro B:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I5E)

(-) Exons   (0, 0)

(no "Exon" information available for 1I5E)

(-) 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:208
 aligned with UPP_BACCL | P70881 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
            UPP_BACCL     2 GKVYVFDHPLIQHKLTYIRDKNTGTKEFRELVDEVATLMAFEITRDLPLEEVEIETPVSKARAKVIAGKKLGVIPILRAGIGMVDGILKLIPAAKVGHIGLYRDPQTLKPVEYYVKLPSDVEERDFIIVDPMLATGGSAVAAIDALKKRGAKSIKFMCLIAAPGRVKAVETAHPDVDIYIAALDERLNDHGYIVPGLGDAGDRLFGTK 209
               SCOP domains d1i5ea_ A: Uracil PRTase, Upp                                                                                                                                                                                    SCOP domains
               CATH domains 1i5eA00 A:2-209  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeeee....eeeee..hhhhhhhhhhhhhh...ee.eeeee........eeeeee........eeeee..ee..hhhhhhhhhhhhhh....eeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i5e A   2 GKVYVFDHPLIQHKLTYIRDKNTGTKEFRELVDEVATLMAFEITRDLPLEEVEIETPVSKARAKVIAGKKLGVIPILRAGIGMVDGILKLIPAAKVGHIGLYRDPQTLKPVEYYVKLPSDVEERDFIIVDPMLATGGSAVAAIDALKKRGAKSIKFMCLIAAPEGVKAVETAHPDVDIYIAALDERLNDHGYIVPGLGDAGDRLFGTK 209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        

Chain B from PDB  Type:PROTEIN  Length:208
 aligned with UPP_BACCL | P70881 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
            UPP_BACCL     2 GKVYVFDHPLIQHKLTYIRDKNTGTKEFRELVDEVATLMAFEITRDLPLEEVEIETPVSKARAKVIAGKKLGVIPILRAGIGMVDGILKLIPAAKVGHIGLYRDPQTLKPVEYYVKLPSDVEERDFIIVDPMLATGGSAVAAIDALKKRGAKSIKFMCLIAAPGRVKAVETAHPDVDIYIAALDERLNDHGYIVPGLGDAGDRLFGTK 209
               SCOP domains d1i5eb_ B: Uracil PRTase, Upp                                                                                                                                                                                    SCOP domains
               CATH domains 1i5eB00 B:2-209  [code=3.40.50.2020, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeeee....eeeee..hhhhhhhhhhhhhh...ee.eeeee........eeeeee........eeeee..ee..hhhhhhhhhhhhhh....eeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i5e B   2 GKVYVFDHPLIQHKLTYIRDKNTGTKEFRELVDEVATLMAFEITRDLPLEEVEIETPVSKARAKVIAGKKLGVIPILRAGIGMVDGILKLIPAAKVGHIGLYRDPQTLKPVEYYVKLPSDVEERDFIIVDPMLATGGSAVAAIDALKKRGAKSIKFMCLIAAPEGVKAVETAHPDVDIYIAALDERLNDHGYIVPGLGDAGDRLFGTK 209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I5E)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UPP_BACCL | P70881)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004845    uracil phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil.
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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0008655    pyrimidine-containing compound salvage    Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.
    GO:0006223    uracil salvage    Any process that generates uracil, 2,4-dioxopyrimidine, from derivatives of it without de novo synthesis.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1upu 1UPU CONTAINS THE UPRTASE FROM T. GONDII WITH UMP