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(-) Description

Title :  STRUCTURE OF THE APO URACIL PHOSPHORIBOSYLTRANSFERASE, 2 MUTANT C128V
 
Authors :  M. A. Schumacher, D. Carter, D. Scott, D. Roos, B. Ullman, R. G. Brennan
Date :  12 May 98  (Deposition) - 18 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Glycosyltransferase, Uprtase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, D. Carter, D. M. Scott, D. S. Roos, B. Ullman, R. G. Brennan
Crystal Structures Of Toxoplasma Gondii Uracil Phosphoribosyltransferase Reveal The Atomic Basis Of Pyrimidine Discrimination And Prodrug Binding.
Embo J. V. 17 3219 1998
PubMed-ID: 9628859  |  Reference-DOI: 10.1093/EMBOJ/17.12.3219
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - URACIL PHOSPHORIBOSYLTRANSFERASE
    Chains: D, C, B, A
    EC Number: 2.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811
    Synonym: UPRTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1PO48Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS D:104 , HOH D:937BINDING SITE FOR RESIDUE PO4 D 799
2AC2SOFTWAREARG C:137 , ALA C:168 , THR C:169 , ALA C:170 , GLY C:171 , SER C:172 , HOH C:904BINDING SITE FOR RESIDUE PO4 C 799
3AC3SOFTWARELYS A:59 , LYS C:104 , ARG C:129 , ARG C:158 , HOH C:979BINDING SITE FOR RESIDUE PO4 C 899
4AC4SOFTWAREARG B:137 , CYS B:167 , ALA B:168 , THR B:169 , ALA B:170 , GLY B:171 , SER B:172 , HOH B:909 , HOH B:991BINDING SITE FOR RESIDUE PO4 B 799
5AC5SOFTWARELYS B:104 , ARG B:129 , ARG B:158 , HOH B:900 , HOH B:935 , LYS D:59BINDING SITE FOR RESIDUE PO4 B 899
6AC6SOFTWAREARG A:137 , ALA A:168 , THR A:169 , ALA A:170 , GLY A:171 , SER A:172 , HOH A:926BINDING SITE FOR RESIDUE PO4 A 799
7AC7SOFTWARELYS A:104 , ARG A:129 , ARG A:158 , HOH A:941 , LYS C:59BINDING SITE FOR RESIDUE PO4 A 899

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BD3)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val D:111 -Arg D:112
2Val D:230 -Pro D:231
3Val C:111 -Arg C:112
4Val C:230 -Pro C:231
5Val B:111 -Arg B:112
6Val B:230 -Pro B:231
7Val A:111 -Arg A:112
8Val A:230 -Pro A:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1BD3)

(-) Exons   (0, 0)

(no "Exon" information available for 1BD3)

(-) 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:224
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:224
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
            UPP_TOXGO    21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1bd3a_ A: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1bd3A00 A:21-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeee.....eeee......eeeeeee.hhhhhhhhhhhh.....eeeeeeee......eeeeeee....hhh.eeeee.......hhhhhhhhhhhhh...hhheeeee....hhhhhhhhhh....eeee...................hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bd3 A  21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:224
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
            UPP_TOXGO    21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1bd3b_ B: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1bd3B00 B:21-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.....eeee.....eeee......eeeeeee.hhhhhhhhhhhh.....eeeeeeee......eeeeeee....hhh.eeeee.......hhhhhhhhhhhhh...hhheeeee.eeehhhhhhhhhh....eeee.eee...............hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bd3 B  21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    


Chain C from PDB  Type:PROTEIN  Length:224
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:224
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
            UPP_TOXGO    21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1bd3c_ C: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1bd3C00 C:21-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeee...eeeeeee.hhhhhhhhhhhh....eeeeeeeee......eeeeeee....hhh.eeeee.......hhhhhhhhhhhhh...hhheeeee....hhhhhhhhhh....eeee...................hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bd3 C  21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    


Chain D from PDB  Type:PROTEIN  Length:224
 aligned with UPP_TOXGO | Q26998 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:224
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
            UPP_TOXGO    21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFEKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGCRIGKILIQRDETTAEPKLIYEKLPADIRDRWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
               SCOP domains d1bd3d_ D: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1bd3D00 D:21-244  [code=3.40.50.2020, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eee....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeee...eeeeeee.hhhhhhhhhhhh.....eeeeeeee......eeeeeee....hhh.eeeee.......hhhhhhhhhhhhh...hhheeeee.eeehhhhhhhhhh....eeee.eee...............hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bd3 D  21 QEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKETPKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVSIVRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERIIFVNILAAPQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM 244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1BD3)

(-) 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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  1bd3
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BD3)