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(-) Description

Title :  PTERIDINE REDUCTASE FROM LEISHMANIA TARENTOLAE COMPLEX WITH NADPH AND MTX
 
Authors :  H. Zhao, T. Bray, M. Ouellette, M. Zhao, R. A. Ferre, D. Matthews, J. M. Whiteley, K. I. Varughese
Date :  16 Apr 03  (Deposition) - 02 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.86
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Pteridine Reductase, Complex, Nadph, Crystal Structure, Mtx, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zhao, T. Bray, M. Ouellette, M. Zhao, R. A. Ferre, D. Matthews, J. M. Whiteley, K. I. Varughese
Structure Of Pteridine Reductase (Ptr1) From Leishmania Tarentolae.
Acta Crystallogr. , Sect. D V. 59 1539 2003
PubMed-ID: 12925782  |  Reference-DOI: 10.1107/S0907444903013131
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE 1
    ChainsA, B, C, D
    EC Number1.1.1.253
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPMALC-2
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePET16B
    FragmentPTERIDINE REDUCTASE
    GenePTR1 OR LTDH
    Organism ScientificLEISHMANIA TARENTOLAE
    Organism Taxid5689
    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, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MTX4Ligand/IonMETHOTREXATE
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ARG A:17 , LEU A:18 , HIS A:38 , ARG A:39 , SER A:40 , ALA A:64 , ASP A:65 , LEU A:66 , SER A:67 , ASN A:109 , ALA A:110 , SER A:111 , SER A:112 , 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:351 , HOH A:400 , HOH A:473 , HOH A:541BINDING SITE FOR RESIDUE NDP A 300
2AC2SOFTWAREGLY B:13 , LYS B:16 , ARG B:17 , LEU B:18 , HIS B:36 , HIS B:38 , ARG B:39 , SER B:40 , ALA B:64 , ASP B:65 , LEU B:66 , SER B:67 , ASN B:109 , ALA B:110 , SER B:111 , SER B:112 , ASP B:142 , MET B:179 , VAL B:180 , TYR B:194 , LYS B:198 , PRO B:224 , GLY B:225 , SER B:227 , VAL B:228 , MTX B:352 , HOH B:412BINDING SITE FOR RESIDUE NDP B 301
3AC3SOFTWAREGLY C:13 , ALA C:15 , ARG C:17 , LEU C:18 , TYR C:37 , HIS C:38 , ARG C:39 , SER C:40 , ASP C:65 , LEU C:66 , SER C:67 , ASN C:109 , ALA C:110 , SER C:111 , SER C:112 , ASP C:142 , SER C:146 , MET C:179 , VAL C:180 , TYR C:194 , LYS C:198 , PRO C:224 , GLY C:225 , LEU C:226 , SER C:227 , VAL C:228 , MTX C:353BINDING SITE FOR RESIDUE NDP C 302
4AC4SOFTWAREGLY D:13 , ALA D:15 , ARG D:17 , LEU D:18 , HIS D:38 , ARG D:39 , SER D:40 , LEU D:66 , SER D:67 , ASN D:109 , ALA D:110 , SER D:111 , SER D:112 , ASP D:142 , MET D:179 , VAL D:180 , TYR D:194 , LYS D:198 , PRO D:224 , GLY D:225 , SER D:227 , VAL D:228 , MTX D:354 , HOH D:428BINDING SITE FOR RESIDUE NDP D 303
5AC5SOFTWAREARG A:17 , SER A:111 , PHE A:113 , PRO A:115 , ASP A:181 , LEU A:188 , TYR A:191 , TYR A:194 , LEU A:226 , LEU A:229 , PRO A:230 , TYR A:241 , NDP A:300 , HOH A:484BINDING SITE FOR RESIDUE MTX A 351
6AC6SOFTWAREARG B:17 , SER B:111 , PHE B:113 , PRO B:115 , ASP B:181 , LEU B:188 , TYR B:191 , TYR B:194 , LEU B:226 , PRO B:230 , MET B:233 , TYR B:241 , NDP B:301BINDING SITE FOR RESIDUE MTX B 352
7AC7SOFTWAREARG C:17 , SER C:111 , PHE C:113 , PRO C:115 , ASP C:181 , LEU C:188 , TYR C:191 , TYR C:194 , LEU C:226 , LEU C:229 , PRO C:230 , MET C:233 , TYR C:241 , NDP C:302BINDING SITE FOR RESIDUE MTX C 353
8AC8SOFTWAREARG D:17 , SER D:111 , PHE D:113 , PRO D:115 , ASP D:181 , TYR D:191 , TYR D:194 , LEU D:229 , PRO D:230 , MET D:233 , TYR D:241 , NDP D:303 , HOH D:509BINDING SITE FOR RESIDUE MTX D 354

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P33)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.PTR1_LEITA182-210
 
 
 
  4A:181-209
B:181-209
C:181-209
D:181-209

(-) Exons   (0, 0)

(no "Exon" information available for 1P33)

(-) 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_LEITA | P42556 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:284
                                    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_LEITA     6 TAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATASFSETDGSVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLRKDAGEGGSSVGDKESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 289
               SCOP domains d1p33a_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p33A00 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............-----------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p33 A   5 TAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATAS------SVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLR-----------DKESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 288
                                    14        24        34        44        54        64        |-     |  84        94       104       114     |   -       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
                                                                                               73     80                                     120         132                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with PTR1_LEITA | P42556 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:286
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283      
           PTR1_LEITA     4 SPTAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATASFSETDGSVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLRKDAGEGGSSVGDKESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 289
               SCOP domains d1p33b_ B: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1p33B00 B:3-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee......ee..------...eehhhhhhhhhhhhhhhhh...eeee.............-----------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhh.........eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p33 B   3 SPTAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATAS------SVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLRK-----------KESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 288
                                    12        22        32        42        52        62        72|      |82        92       102       112        |-         -|      142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
                                                                                                 73     80                                      121         133                                                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:268
 aligned with PTR1_LEITA | P42556 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:285
                                    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_LEITA     5 PTAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATASFSETDGSVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLRKDAGEGGSSVGDKESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 289
               SCOP domains d1p33c_ C: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1p33C00 C:4-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee..........------....hhhhhhhhhhhhhhhhhh...eeee.............-----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p33 C   4 PTAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATAS------SVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLRK-----------KESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 288
                                    13        23        33        43        53        63        73      | 83        93       103       113       | -       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
                                                                                                73     80                                      121         133                                                                                                                                                           

Chain D from PDB  Type:PROTEIN  Length:268
 aligned with PTR1_LEITA | P42556 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:284
                                    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_LEITA     6 TAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATASFSETDGSVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLRKDAGEGGSSVGDKESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 289
               SCOP domains d1p33d_ D: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1p33D00 D:5-288 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) --------adh_short_C2-1p33D01 D:13-284                                                                                                                                                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) --------adh_short_C2-1p33D02 D:13-284                                                                                                                                                                                                                                                   ---- Pfam domains (2)
           Pfam domains (3) --------adh_short_C2-1p33D03 D:13-284                                                                                                                                                                                                                                                   ---- Pfam domains (3)
           Pfam domains (4) --------adh_short_C2-1p33D04 D:13-284                                                                                                                                                                                                                                                   ---- Pfam domains (4)
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh...ee.............------....hhhhhhhhhhhhhhh......eeee.............----------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:181-209    ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p33 D   5 TAPVALVTGAAKRLGSSIAEALHAEGYTVCLHYHRSAADASTLAATLNARRPNSAITVQADLSNVATAS------SVPVTLFSRCSALVDACYMHWGRCDVLVNNASSFYPTPLLRK----------DKESLEVAAADLFGSNAIAPYFLIKAFAQRVADTRAEQRGTSYSIVNMVDAMTSQPLLGYTMYTMAKEALEGLTRSAALELASLQIRVNGVSPGLSVLPDDMPFSVQEDYRRKVPLYQRNSSAEEVSDVVIFLCSPKAKYITGTCIKVDGGYSLTRA 288
                                    14        24        34        44        54        64        |-     |  84        94       104       114      |  -       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    
                                                                                               73     80                                      121        132                                                                                                                                                            

   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  (1, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PTR1_LEITA | P42556)
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.
biological process
    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: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)

(no "Entries Sharing at Least One Protein Chain" available for 1P33)

(-) Related Entries Specified in the PDB File

1e7w PTR1 FROM LEISHMANIA MAJOR COMPLEX WITH MTX
1e92 PTR1 FROM LEISHMANIA MAJOR COMPLEX WITH DHB