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(-) Description

Title :  STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE GTP COMPLEX 2 MUTANT C128V
 
Authors :  M. A. Schumacher, C. J. Bashor, K. Otsu, S. Zu, R. Parry, B. Ulmman, R. G. Brennan
Date :  16 Jul 01  (Deposition) - 10 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Glycosyltransferase, Uprtase, Gtp Activated, Tetramer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, C. J. Bashor, M. H. Song, K. Otsu, S. Zhu, R. J. Parry, B. Ullman, R. G. Brennan
The Structural Mechanism Of Gtp Stabilized Oligomerization And Catalytic Activation Of The Toxoplasma Gondii Uracil Phosphoribosyltransferase.
Proc. Natl. Acad. Sci. Usa V. 99 78 2002
PubMed-ID: 11773618  |  Reference-DOI: 10.1073/PNAS.012399599
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, D, C
    EC Number: 2.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PBACE
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2PO48Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG D:112 , ALA D:113 , ASP D:235 , GLY D:237BINDING SITE FOR RESIDUE PO4 D 799
02AC2SOFTWAREARG B:112 , ALA B:113 , ASP B:235BINDING SITE FOR RESIDUE PO4 B 800
03AC3SOFTWAREARG D:137 , ALA D:168 , THR D:169 , ALA D:170 , GLY D:171 , SER D:172 , HOH D:825BINDING SITE FOR RESIDUE PO4 D 801
04AC4SOFTWAREARG C:112 , ALA C:113 , ASP C:235BINDING SITE FOR RESIDUE PO4 C 802
05AC5SOFTWAREARG C:137 , ALA C:168 , THR C:169 , ALA C:170 , GLY C:171 , SER C:172 , HOH C:815BINDING SITE FOR RESIDUE PO4 C 803
06AC6SOFTWAREALA B:168 , THR B:169 , ALA B:170 , GLY B:171 , SER B:172 , HOH B:830BINDING SITE FOR RESIDUE PO4 B 804
07AC7SOFTWAREVAL A:111 , ARG A:112 , ALA A:113 , ASP A:235 , HOH A:843 , TYR D:148 , LYS D:150BINDING SITE FOR RESIDUE PO4 A 805
08AC8SOFTWAREARG A:137 , ALA A:168 , THR A:169 , ALA A:170 , GLY A:171 , SER A:172 , HOH A:809BINDING SITE FOR RESIDUE PO4 A 806
09AC9SOFTWAREGLN A:44 , TYR A:65 , ARG A:68 , LYS B:59 , LEU C:78 , LEU C:81 , PHE C:101 , TYR C:102 , SER C:103 , ILE C:105 , ARG C:129 , ARG C:158BINDING SITE FOR RESIDUE GTP C 300
10BC1SOFTWARELEU B:78 , LEU B:81 , PHE B:101 , TYR B:102 , SER B:103 , LYS B:104 , ILE B:105 , ARG B:129 , ARG B:158 , HOH B:805 , LYS C:59 , GLN D:44 , TYR D:65 , ARG D:68 , HOH D:833BINDING SITE FOR RESIDUE GTP B 301
11BC2SOFTWARELYS A:59 , GLN B:44 , TYR B:65 , ARG B:68 , LEU D:78 , LEU D:81 , PHE D:101 , TYR D:102 , SER D:103 , LYS D:104 , ILE D:105 , ARG D:129 , ARG D:158 , HOH D:804BINDING SITE FOR RESIDUE GTP D 302
12BC3SOFTWARELEU A:78 , PHE A:101 , LYS A:104 , CYS A:125 , ARG A:129 , ARG A:158 , HOH A:807 , HOH A:814 , HOH A:841 , GLN C:44 , TYR C:65 , ARG C:68 , HOH C:828 , LYS D:59BINDING SITE FOR RESIDUE GTP A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:230 -Pro A:231
2Val B:230 -Pro B:231
3Val D:230 -Pro D:231
4Val C:230 -Pro C:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JLR)

(-) 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:235
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
            UPP_TOXGO    10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1jlra_ A: Uracil PRTase, Upp                                                                                                                                                                                                               SCOP domains
               CATH domains 1jlrA00 A:10-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeeeee...eeeeee.hhhhhhhhhhhhhh....eeeeeee........eeeeee...hhhhheeeee..ee..hhhhhhhhhhhhhh..hhh.eeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jlr A  10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
            UPP_TOXGO    10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1jlrb_ B: Uracil PRTase, Upp                                                                                                                                                                                                               SCOP domains
               CATH domains 1jlrB00 B:10-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...eeeeee..hhhhhhhhhhhhh....eeeeeeee......eeeeeee...hhhhheeeee..ee..hhhhhhhhhhhhhhh.hhh.eeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jlr B  10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     


Chain C from PDB  Type:PROTEIN  Length:235
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
            UPP_TOXGO    10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1jlrc_ C: Uracil PRTase, Upp                                                                                                                                                                                                               SCOP domains
               CATH domains 1jlrC00 C:10-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeeeee...eeeeee.hhhhhhhhhhhhhh....eeeeeeee......eeeeeee...hhhhheeeee..ee..hhhhhhhhhhhhh...hhh.eeee..eehhhhhhhhhhhh...eeee.ee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jlr C  10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     


Chain D from PDB  Type:PROTEIN  Length:235
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
            UPP_TOXGO    10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1jlrd_ D: Uracil PRTase, Upp                                                                                                                                                                                                               SCOP domains
               CATH domains 1jlrD00 D:10-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh..eee...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...eeeeee.hhhhhhhhhhhhhh....eeeeeee........eeeeee...hhhhheeeee..ee..hhhhhhhhhhhhhhh.hhh.eeeeeeeehhhhhhhhhhhh...eeeeeee..ee.....ee....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jlr D  10 LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (UPP_TOXGO | Q26998)
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: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.

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  1jlr
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  UPP_TOXGO | Q26998
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 Related Entries

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

UniProtKB/Swiss-Prot
        UPP_TOXGO | Q26998: 1bd3 1bd4 1jls 1upf 1upu

(-) Related Entries Specified in the PDB File

1bd3 T. GONDII APO UPRTASE
1bd4 T. GONDII UPRT-URACIL COMPLEX
1upf T. GONDII UPRT-5-FLUOROURACIL COMPLEX
1upu T. GONDII UPRT-UMP COMPLEX