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(-) Description

Title :  STRUCTURE OF THE URACIL PHOSPHORIBOSYLTRANSFERASE, MUTANT C128V BOUND TO THE DRUG 5-FLUOROURACIL
 
Authors :  M. A. Schumacher, D. Carter, D. Scott, D. Roos, B. Ullman, R. G. Brennan
Date :  17 Jun 98  (Deposition) - 22 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Glycosyltransferase, Phosphoribosyltransferase (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  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
2URF4Ligand/Ion5-FLUOROURACIL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG D:137 , CYS D:167 , ALA D:168 , THR D:169 , ALA D:170 , GLY D:171 , SER D:172BINDING SITE FOR RESIDUE SO4 D 799
02AC2SOFTWARELYS B:150 , VAL D:111 , ARG D:112 , ALA D:113 , GLY D:237 , HOH D:1005 , HOH D:1019BINDING SITE FOR RESIDUE SO4 D 599
03AC3SOFTWARELYS B:59 , ARG D:129 , ARG D:158BINDING SITE FOR RESIDUE SO4 D 899
04AC4SOFTWAREARG C:137 , ALA C:168 , THR C:169 , ALA C:170 , GLY C:171 , SER C:172 , HOH C:1013 , HOH C:1032 , HOH C:1069BINDING SITE FOR RESIDUE SO4 C 799
05AC5SOFTWAREARG C:112 , ALA C:113 , GLY C:237BINDING SITE FOR RESIDUE SO4 C 599
06AC6SOFTWARELYS A:59 , ARG C:129 , ARG C:158BINDING SITE FOR RESIDUE SO4 C 899
07AC7SOFTWAREARG B:112 , ALA B:113 , GLY B:237 , HOH B:1011 , HOH B:1034BINDING SITE FOR RESIDUE SO4 B 599
08AC8SOFTWAREARG B:137 , CYS B:167 , ALA B:168 , THR B:169 , ALA B:170 , GLY B:171 , SER B:172 , HOH B:1006BINDING SITE FOR RESIDUE SO4 B 799
09AC9SOFTWAREARG B:129 , ARG B:158 , HOH B:1000 , HOH B:1005 , LYS D:59BINDING SITE FOR RESIDUE SO4 B 899
10BC1SOFTWAREARG A:137 , ALA A:168 , THR A:169 , ALA A:170 , GLY A:171 , SER A:172BINDING SITE FOR RESIDUE SO4 A 799
11BC2SOFTWAREARG A:129 , ARG A:158 , LYS C:59BINDING SITE FOR RESIDUE SO4 A 899
12BC3SOFTWAREARG A:112 , ALA A:113 , GLY A:237BINDING SITE FOR RESIDUE SO4 A 599
13BC4SOFTWAREMET D:166 , ALA D:168 , TYR D:227 , TYR D:228 , ILE D:229 , GLY D:234 , PHE D:236BINDING SITE FOR RESIDUE URF D 999
14BC5SOFTWAREMET C:166 , ALA C:168 , TYR C:227 , TYR C:228 , ILE C:229 , GLY C:234 , ASP C:235 , PHE C:236 , HOH C:1003BINDING SITE FOR RESIDUE URF C 999
15BC6SOFTWAREMET B:166 , ALA B:168 , TYR B:227 , TYR B:228 , ILE B:229 , ILE B:233 , GLY B:234 , ASP B:235 , PHE B:236 , HOH B:1002BINDING SITE FOR RESIDUE URF B 999
16BC7SOFTWAREMET A:166 , ALA A:168 , TYR A:227 , TYR A:228 , ILE A:229 , GLY A:234 , ASP A:235 , PHE A:236 , HOH A:1013 , HOH A:1045BINDING SITE FOR RESIDUE URF A 999

(-) SS Bonds  (0, 0)

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

(-) 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 1UPF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UPF)

(-) 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 d1upfa_ A: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1upfA00 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.......hhhhhhhhhhhh....hhheeeee.eeehhhhhhhhhh....eeee.eee...............hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upf 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 d1upfb_ B: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1upfB00 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.....eeeeeee........eeeeee....hhh.eeeee.......hhhhhhhhhhhh....hhheeeee.eeehhhhhhhhhhh...eeee.eee...............hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upf 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 d1upfc_ C: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1upfC00 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
                 1upf 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 d1upfd_ D: Uracil PRTase, Upp                                                                                                                                                                                                    SCOP domains
               CATH domains 1upfD00 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
                 1upf 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)
    → 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 1UPF)

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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