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(-) Description

Title :  ONE ACTIVE SITE, TWO MODES OF REDUCTION CORRELATE THE MECHANISM OF LEISHMANIA PTERIDINE REDUCTASE WITH PTERIN METABOLISM AND ANTIFOLATE DRUG RESISTANCE IN TRPANOSOMES
 
Authors :  D. G. Gourley, W. N. Hunter
Date :  11 Sep 00  (Deposition) - 06 Sep 01  (Release) - 21 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dihydrofolate Reductase, Pteridine Reductase, Shortchain Dehydrogenase, Methotrexate Resistance, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. G. Gourley, A. Schuttelkopf, G. Leonard, J. Luba, L. Hardy, S. Beverley, W. N. Hunter
Pteridine Reductase Mechanism Correlates Pterin Metabolism With Drug Resistance In Trypanosomatid Parasites.
Nat. Struct. Biol. V. 8 521 2001
PubMed-ID: 11373620  |  Reference-DOI: 10.1038/88584

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.253
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector: PET15B
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: CC-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MTX2Ligand/IonMETHOTREXATE
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MTX4Ligand/IonMETHOTREXATE
3NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:17 , LEU A:18 , HIS A:36 , TYR A:37 , HIS A:38 , ARG A:39 , SER A:40 , ALA A:64 , ASP A:65 , LEU A:66 , ASN A:109 , ALA A:110 , SER A:111 , ASP A:142 , MET A:179 , VAL A:180 , ASP A:181 , TYR A:194 , LYS A:198 , PRO A:224 , GLY A:225 , LEU A:226 , SER A:227 , MTX A:301 , HOH A:2005 , HOH A:2008 , HOH A:2131 , HOH A:2253 , HOH A:2254 , HOH A:2255 , HOH A:2256 , HOH A:2257BINDING SITE FOR RESIDUE NDP A 300
2AC2SOFTWAREARG A:17 , SER A:111 , PHE A:113 , PRO A:115 , LEU A:188 , TYR A:191 , TYR A:194 , LEU A:226 , LEU A:229 , ASP A:232 , MET A:233 , NDP A:300 , EDO A:1290 , HOH A:2192 , HOH A:2198 , HOH A:2258 , HOH A:2259 , HOH A:2260 , HOH A:2261 , HOH A:2263BINDING SITE FOR RESIDUE MTX A 301
3AC3SOFTWAREGLY A:199 , GLU A:202 , ARG A:206 , HOH A:2264 , GLY B:199 , GLU B:202 , ARG B:206BINDING SITE FOR RESIDUE EDO A1289
4AC4SOFTWAREPHE A:113 , ASP A:181 , TYR A:194 , MTX A:301 , HOH A:2190 , HOH A:2265 , ARG B:287 , HOH B:2198BINDING SITE FOR RESIDUE EDO A1290
5AC5SOFTWAREARG B:17 , LEU B:18 , HIS B:36 , TYR B:37 , HIS B:38 , ARG B:39 , SER B:40 , ALA B:64 , ASP B:65 , LEU B:66 , ASN B:109 , ALA B:110 , SER B:111 , ASP B:142 , MET B:179 , VAL B:180 , ASP B:181 , TYR B:194 , LYS B:198 , PRO B:224 , GLY B:225 , SER B:227 , MTX B:301 , HOH B:2006 , HOH B:2135 , HOH B:2203 , HOH B:2204 , HOH B:2205 , HOH B:2206 , HOH B:2207 , HOH B:2208BINDING SITE FOR RESIDUE NDP B 300
6AC6SOFTWAREARG B:17 , SER B:111 , PHE B:113 , PRO B:115 , LEU B:188 , LEU B:189 , TYR B:191 , TYR B:194 , LEU B:226 , HIS B:241 , NDP B:300 , EDO B:1289 , HOH B:2130 , HOH B:2209 , HOH B:2210BINDING SITE FOR RESIDUE MTX B 301
7AC7SOFTWAREARG A:287 , ASP B:181 , MTX B:301 , HOH B:2134 , HOH B:2150BINDING SITE FOR RESIDUE EDO B1289

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E7W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E7W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E7W)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.PTR1_LEIMA181-209
 		  2A:181-209
B:181-209
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.PTR1_LEIMA181-209
 		  4A:181-209
B:181-209

(-) Exons   (0, 0)

(no "Exon" information available for 1E7W)

(-) 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:267
 aligned with PTR1_LEIMA | Q01782 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:284
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
           PTR1_LEIMA     5 TVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPVSGADGSAPVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLRNDEDGHEPCVGDREAMETATADLFGSNAIAPYFLIKAFAHRFAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDDMPPAVWEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 288
               SCOP domains d1e7wa_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1e7wA00 A:5-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee............----....hhhhhhhhhhhhhhhhhh...eeee...........-------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e7w A   5 TVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPVS----SAPVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLL-------------REAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDDMPPAVWEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 288
                                    14        24        34        44        54        64        74|    |  84        94       104       114    |    -       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
                                                                                                 75   80                                    119           133                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with PTR1_LEIMA | Q01782 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:283
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   
           PTR1_LEIMA     6 VPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPVSGADGSAPVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLRNDEDGHEPCVGDREAMETATADLFGSNAIAPYFLIKAFAHRFAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDDMPPAVWEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 288
               SCOP domains d1e7wb_ B: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1e7wB00 B:6-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.........---------..hhhhhhhhhhhhhhhhhh...eeee............----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......------hhhhhh..........hhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e7w B   6 VPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATA---------PVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLR----------GDREAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVD------WEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 288
                                    15        25        35        45        55        65      |  -      | 85        95       105       115    |    -     | 135       145       155       165       175       185       195       205       215       225     |   -  |    245       255       265       275       285   
                                                                                             72        82                                   120        131                                                                                                 231    238
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E7W)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PTR1_LEIMA | Q01782)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0047040    pteridine reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + 2 NADP(+) = biopterin + 2 H(+) + 2 NADPH.
    GO:0004799    thymidylate synthase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
biological process
    GO:0034599    cellular response to oxidative stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0019889    pteridine metabolic process    The chemical reactions and pathways involving pteridine, pyrazino(2,3-dipyrimidine), the parent structure of pterins and the pteroyl group.
    GO:0031427    response to methotrexate    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methotrexate stimulus. Methotrexate is 4-amino-10-methylformic acid, a folic acid analogue that is a potent competitive inhibitor of dihydrofolate reductase.
    GO:0006729    tetrahydrobiopterin biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.

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  1e7w
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  PTR1_LEIMA | Q01782
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  1.1.1.253
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 Related Entries

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

UniProtKB/Swiss-Prot
        PTR1_LEIMA | Q01782: 1e92 1w0c 2bf7 2bfa 2bfm 2bfo 2bfp 2qhx 3h4v 5l42 5l4n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1E7W)