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(-) Description

Title :  SYMMETRIC SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE WITH BOUND PRPP AND GTP
 
Authors :  A. Kadziola
Date :  09 Feb 09  (Deposition) - 01 Sep 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Uracil, Phosphoribosyltransferase, Allosteric Regulation, Sulfolobus Solfataricus, Prpp, Gtp, Glycosyltransferase, Magnesium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Christoffersen, A. Kadziola, E. Johansson, M. Rasmussen, M. Willemoes, K. F. Jensen
Structural And Kinetic Studies Of The Allosteric Transition In Sulfolobus Solfataricus Uracil Phosphoribosyltransferase: Permanent Activation By Engineering Of The C-Terminus
J. Mol. Biol. V. 393 464 2009
PubMed-ID: 19683539  |  Reference-DOI: 10.1016/J.JMB.2009.08.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL PHOSPHORIBOSYLTRANSFERASE
    ChainsA
    EC Number2.4.2.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPLFS2
    Expression System StrainNF1830
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSSO0231, UPP
    Organism ScientificSULFOLOBUS SOLFATARICUS
    Organism Taxid2287
    SynonymUMP PYROPHOSPHORYLASE, UPRTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3PRP1Ligand/IonALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PRP4Ligand/IonALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:26 , ASN A:27 , LYS A:30 , ARG A:34 , ARG A:37 , LYS A:91 , PRO A:94 , MG A:302 , HOH A:406 , HOH A:410BINDING SITE FOR RESIDUE GTP A 301
2AC2SOFTWAREGTP A:301BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWARELEU A:79 , ARG A:80 , ALA A:81 , ARG A:105 , LYS A:125 , ASP A:140 , MET A:142 , ALA A:144 , THR A:145 , ALA A:146 , SER A:147 , THR A:148 , ASP A:209 , HOH A:402BINDING SITE FOR RESIDUE PRP A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:79 -Arg A:80
2Leu A:204 -Pro A:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VST)

(-) 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:215
 aligned with UPP_SULSO | Q980Q4 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     
            UPP_SULSO     2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
               SCOP domains d1vsta_ A: Uracil PRTase, Upp                                                                                                                                                                                           SCOP domains
               CATH domains 1vstA00 A:2-216  [code=3.40.50.2020, no name defined]                                                                                                                                                                   CATH domains
               Pfam domains -----------------------------------------------------------Pribosyltran-1vstA01 A:61-170                                                                                 ---------------------------------------------- Pfam domains
         Sec.struct. author .eee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeeeehhhhh.eeeeee..hhhhhhhhhh......eeeeeeeee.............eeeeeee.........eeeee..ee..hhhhhhhhhhhhhhh..eeeee..eeehhhhhhhhhhh...eeee.eee.ee.....ee....hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vst A   2 PLYVIDKPITLHILTQLRDKYTDQINFRKNLVRLGRILGYEISNTLDYEIVEVETPLGVKTKGVDITDLNNIVIINILRAAVPLVEGLLKAFPKARQGVIGASRVEVDGKEVPKDMDVYIYYKKIPDIRAKVDNVIIADPMIATASTMLKVLEEVVKANPKRIYIVSIISSEYGVNKILSKYPFIYLFTVAIDPELNNKGYILPGLGDAGDRAFG 216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211     

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (UPP_SULSO | Q980Q4)
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.
    GO:0004849    uridine kinase activity    Catalysis of the reaction: ATP + uridine = ADP + UMP.
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:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UPP_SULSO | Q980Q41xtt 1xtu 1xtv 3g6w

(-) Related Entries Specified in the PDB File

1xtt SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE (UMP)
1xtu SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH URIDINE 5'-MONOPHOSPHATE (UMP) AND CYTIDINE 5' -TRIPHOSPHATE (CTP)
1xtv SULFOLOBUS SOLFATARICUS URACIL PHOSPHORIBOSYLTRANSFERASE WITH URIDINE 5'-MONOPHOSPHATE (UMP) BOUND TO HALF OF THE SUBUNITS
3g6w