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(-) Description

Title :  LEISHMANIA MAJOR PTERIDINE REDUCTASE 1 IN COMPLEX WITH NADPH
 
Authors :  A. W. Schuettelkopf, W. N. Hunter
Date :  10 Dec 04  (Deposition) - 31 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pteridine Reductase, Trypanosomatids, Drug Resistance, Pterin Salvage, Short-Chain Dehydrogenase/Reductase, Methotrexate Resistance, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. W. Schuettelkopf, L. W. Hardy, S. M. Beverley, W. N. Hunter
Structures Of Leishmania Major Pteridine Reductase Complexes Reveal The Active Site Features Important For Ligand Binding And To Guide Inhibitor Design
J. Mol. Biol. V. 352 105 2005
PubMed-ID: 16055151  |  Reference-DOI: 10.1016/J.JMB.2005.06.076

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE 1
    ChainsA, B, C, D
    EC Number1.5.1.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET 15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Organism ScientificLEISHMANIA MAJOR
    Organism Taxid5664
    SynonymH REGION METHOTREXATE RESISTANCE PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG 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 , SER A:112 , ASP A:142 , MET A:179 , VAL A:180 , ASP A:181 , LYS A:198 , PRO A:224 , GLY A:225 , LEU A:226 , SER A:227 , HOH A:2001 , HOH A:2046 , HOH A:2113 , HOH A:2114 , HOH A:2115 , HOH B:2070 , HOH B:2071BINDING SITE FOR RESIDUE NDP A1289
02AC2SOFTWAREASN A:68 , ILE A:149 , HOH A:2116 , ASN B:68BINDING SITE FOR RESIDUE EDO A1290
03AC3SOFTWAREGLY A:199 , GLU A:202 , ARG A:206 , GLY B:199 , GLU B:202 , ARG B:206BINDING SITE FOR RESIDUE EDO A1291
04AC4SOFTWAREASP A:181 , TYR A:194 , HOH A:2081 , HOH A:2118 , ARG D:287BINDING SITE FOR RESIDUE EDO A1292
05AC5SOFTWAREARG 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 , SER B:112 , ASP B:142 , MET B:179 , VAL B:180 , ASP B:181 , LYS B:198 , PRO B:224 , GLY B:225 , LEU B:226 , SER B:227 , HOH B:2098 , HOH B:2099 , HOH B:2100 , HOH B:2101 , HOH B:2102 , HOH B:2103 , HOH B:2104BINDING SITE FOR RESIDUE NDP B1289
06AC6SOFTWAREASP B:181 , LEU B:188 , HOH B:2058 , HOH B:2066 , ARG C:287BINDING SITE FOR RESIDUE EDO B1290
07AC7SOFTWAREARG C:17 , LEU C:18 , HIS C:36 , HIS C:38 , ARG C:39 , SER C:40 , ALA C:64 , ASP C:65 , LEU C:66 , ASN C:109 , ALA C:110 , SER C:111 , SER C:112 , ASP C:142 , MET C:179 , VAL C:180 , ASP C:181 , LYS C:198 , PRO C:224 , GLY C:225 , LEU C:226 , SER C:227 , HOH C:2003 , HOH C:2046 , HOH C:2078 , HOH C:2079 , HOH C:2080BINDING SITE FOR RESIDUE NDP C1289
08AC8SOFTWAREARG B:287 , ASP C:181 , TYR C:194 , HOH C:2045 , HOH C:2053BINDING SITE FOR RESIDUE EDO C1290
09AC9SOFTWAREARG D:17 , LEU D:18 , HIS D:36 , HIS D:38 , ARG D:39 , SER D:40 , ALA D:64 , ASP D:65 , LEU D:66 , ASN D:109 , ALA D:110 , SER D:111 , SER D:112 , ASP D:142 , MET D:179 , VAL D:180 , ASP D:181 , LYS D:198 , PRO D:224 , GLY D:225 , LEU D:226 , SER D:227 , HOH D:2026 , HOH D:2049 , HOH D:2071 , HOH D:2072 , HOH D:2073BINDING SITE FOR RESIDUE NDP D1289
10BC1SOFTWAREARG A:287 , ASP D:181 , LEU D:188 , TYR D:194 , HOH D:2042 , HOH D:2046 , HOH D:2075BINDING SITE FOR RESIDUE EDO D1290

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BFO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BFO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BFO)

(-) PROSITE Motifs  (1, 4)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BFO)

(-) 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:267
 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 d2bfoa_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bfoA00 A:6-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee...........------...hhhhhhhhhhhhhhhhhh...eeee............----------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bfo A   6 VPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPV------APVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLR----------GDREAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDDMPPAVWEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 288
                                    15        25        35        45        55        65        |-     |  85        95       105       115    |    -     | 135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   
                                                                                               74     81                                    120        131                                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:266
 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 d2bfob_ B: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bfoB00 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.............-----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bfo B   6 VPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPV------APVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLRN-----------REAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDDMPPAVWEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 288
                                    15        25        35        45        55        65        |-     |  85        95       105       115     |   -       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   
                                                                                               74     81                                     121         133                                                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:255
 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 d2bfoc_ C: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2bfoC00 C:6-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.........---------..hhhhhhhhhhhhhhhhhh...eeee............-----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......--------.hhhhh........hhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bfo C   6 VPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATA---------PVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLR-----------DREAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVD--------GHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 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         132                                                                                                231      240                                                

Chain D from PDB  Type:PROTEIN  Length:256
 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 d2bfod_ D: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2bfoD00 D:5-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee..........-------...hhhhhhhhhhhhhhhhhh...eeee............------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......---------.hhhhh........hhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bfo D   5 TVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAP-------APVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLR------------REAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLV---------GHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTCVKVDGGYSLTRA 288
                                    14        24        34        44        54        64        |-      | 84        94       104       114     |   -       134       144       154       164       174       184       194       204       214       224     |   -     | 244       254       264       274       284    
                                                                                               73      81                                    120          133                                                                                              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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BFO)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        PTR1_LEIMA | Q017821e7w 1e92 1w0c 2bf7 2bfa 2bfm 2bfp 2qhx 3h4v 5l42 5l4n

(-) Related Entries Specified in the PDB File

2bf7 LEISHMANIA MAJOR PTERIDINE REDUCTASE 1 IN COMPLEX WITH NADP AND BIOPTERIN
2bfa LEISHMANIA MAJOR PTERIDINE REDUCTASE 1 IN COMPLEX WITH NADP AND CB3717
2bfm LEISHMANIA MAJOR PTERIDINE REDUCTASE 1 IN COMPLEX WITH NADP AND TRIMETHOPRIM
2bfp LEISHMANIA MAJOR PTERIDINE REDUCTASE 1 IN COMPLEX WITH NADP AND TETRAHYDROBIOPTERIN