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(-) Description

Title :  CRYSTAL STRUCTURE OF INHIBITOR COMPLEX OF PUTATIVE PTERIDINE REDUCTASE 2 (PTR2) FROM TRYPANOSOMA CRUZI
 
Authors :  N. Schormann, B. Pal, O. Senkovich, M. Carson, A. Howard, C. Smith, L. Delucas, D. Chattopadhyay
Date :  02 Oct 02  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sdr Topology, Protein-Inhibitor Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, B. Pal, O. Senkovich, M. Carson, A. Howard, C. Smith, L. Delucas, D. Chattopadhyay
Crystal Structure Of Trypanosoma Cruzi Pteridine Reductase 2 In Complex With A Substrate And An Inhibitor.
J. Struct. Biol. V. 152 64 2005
PubMed-ID: 16168672  |  Reference-DOI: 10.1016/J.JSB.2005.07.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE 2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: B834PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PTERIDINE REDUCTASE
    Gene: PTR2
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 5693
    Strain: SYLVIO, X10

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2MTX4Ligand/IonMETHOTREXATE
3NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:21 , ARG A:22 , ILE A:23 , ARG A:43 , HIS A:44 , SER A:45 , GLY A:69 , ASP A:70 , LEU A:71 , SER A:72 , ASN A:101 , ALA A:102 , SER A:103 , GLU A:131 , LEU A:167 , CYS A:168 , TYR A:182 , LYS A:186 , PRO A:212 , GLY A:213 , SER A:215 , LEU A:216 , MTX A:1278 , HOH A:1291 , HOH A:1294 , HOH A:1336BINDING SITE FOR RESIDUE NDP A 1277
2AC2SOFTWAREARG A:22 , SER A:103 , TYR A:105 , ASP A:169 , LEU A:176 , TYR A:182 , LEU A:214 , LEU A:216 , MSE A:221 , THR A:225 , TYR A:229 , NDP A:1277 , HOH A:1331BINDING SITE FOR RESIDUE MTX A 1278
3AC3SOFTWAREARG B:22 , ILE B:23 , TYR B:42 , ARG B:43 , HIS B:44 , SER B:45 , GLY B:69 , ASP B:70 , LEU B:71 , SER B:72 , ASN B:101 , ALA B:102 , SER B:103 , ALA B:104 , LEU B:167 , CYS B:168 , ASP B:169 , TYR B:182 , LYS B:186 , PRO B:212 , GLY B:213 , SER B:215 , LEU B:216 , MTX B:2278 , HOH B:2286 , HOH B:2292 , HOH B:2293 , HOH B:2336BINDING SITE FOR RESIDUE NDP B 2277
4AC4SOFTWAREARG B:22 , SER B:103 , TYR B:105 , ASP B:169 , LEU B:176 , PHE B:179 , TYR B:182 , LEU B:214 , LEU B:216 , MSE B:221 , THR B:225 , TYR B:229 , NDP B:2277BINDING SITE FOR RESIDUE MTX B 2278
5AC5SOFTWAREARG C:21 , ARG C:22 , ILE C:23 , ARG C:43 , HIS C:44 , SER C:45 , GLY C:69 , ASP C:70 , LEU C:71 , SER C:72 , ASN C:101 , ALA C:102 , SER C:103 , LEU C:167 , CYS C:168 , TYR C:182 , LYS C:186 , PRO C:212 , GLY C:213 , SER C:215 , LEU C:216 , MTX C:3278 , HOH C:3289 , HOH C:3290 , HOH C:3291 , HOH C:3323 , HOH C:3349 , HOH C:3373BINDING SITE FOR RESIDUE NDP C 3277
6AC6SOFTWAREARG C:22 , SER C:103 , TYR C:105 , ASP C:169 , LEU C:176 , TYR C:182 , LEU C:214 , LEU C:216 , THR C:225 , TYR C:229 , NDP C:3277 , HOH C:3326 , HOH C:3370BINDING SITE FOR RESIDUE MTX C 3278
7AC7SOFTWAREARG D:21 , ARG D:22 , ILE D:23 , TYR D:42 , ARG D:43 , HIS D:44 , SER D:45 , GLY D:69 , ASP D:70 , LEU D:71 , SER D:72 , ASN D:101 , ALA D:102 , SER D:103 , GLU D:131 , LEU D:167 , CYS D:168 , TYR D:182 , LYS D:186 , PRO D:212 , GLY D:213 , SER D:215 , LEU D:216 , MTX D:4278 , HOH D:4286 , HOH D:4287 , HOH D:4293 , HOH D:4317 , HOH D:4318 , HOH D:4345 , HOH D:4381BINDING SITE FOR RESIDUE NDP D 4277
8AC8SOFTWAREARG D:22 , SER D:103 , TYR D:105 , LEU D:176 , PHE D:179 , TYR D:182 , LEU D:214 , LEU D:216 , MSE D:221 , THR D:225 , TYR D:229 , NDP D:4277 , HOH D:4313 , HOH D:4367 , HOH D:4371BINDING SITE FOR RESIDUE MTX D 4278

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MXF)

(-) 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:247
 aligned with Q8I814_TRYCR | Q8I814 from UniProtKB/TrEMBL  Length:276

    Alignment length:266
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
         Q8I814_TRYCR    11 CPAAIITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLPGDDTNGAAEAKPIDAQVAELFGSNAVAPLFLIRAFARRQGEGGAWRSRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADVIAFLVSKDAGYITGTTLKVDGGLILARA 276
               SCOP domains d1mxfa_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxfA00 A:11-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............----------.hhhhhhhhhhhhhhhhhhhhhhhhhhh.---------.eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxf A  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP----------KPIDAQVAELFGSNAVAPLFLIRAFARRQ---------NLSVVNLCDAmTDLPLPGFCVYTmAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAmPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -  |    130       140       150|        -|      170|      180   |   190       200       210       220|      230       240       250       260       270      
                                                                                                                               112        123                         151       161       171-MSE      184-MSE                              221-MSE                                                   


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Q8I814_TRYCR | Q8I814 from UniProtKB/TrEMBL  Length:276

    Alignment length:266
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
         Q8I814_TRYCR    11 CPAAIITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLPGDDTNGAAEAKPIDAQVAELFGSNAVAPLFLIRAFARRQGEGGAWRSRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADVIAFLVSKDAGYITGTTLKVDGGLILARA 276
               SCOP domains d1mxfb_ B: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxfB00 B:11-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhhhhh...eeee............----------.hhhhhhhhhhhhhhhhhhhhhhhhhhh.---------.eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxf B  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP----------KPIDAQVAELFGSNAVAPLFLIRAFARRQ---------NLSVVNLCDAmTDLPLPGFCVYTmAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAmPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -  |    130       140       150|        -|      170|      180   |   190       200       210       220|      230       240       250       260       270      
                                                                                                                               112        123                         151       161       171-MSE      184-MSE                              221-MSE                                                   


Chain C from PDB  Type:PROTEIN  Length:247
 aligned with Q8I814_TRYCR | Q8I814 from UniProtKB/TrEMBL  Length:276

    Alignment length:266
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
         Q8I814_TRYCR    11 CPAAIITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLPGDDTNGAAEAKPIDAQVAELFGSNAVAPLFLIRAFARRQGEGGAWRSRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADVIAFLVSKDAGYITGTTLKVDGGLILARA 276
               SCOP domains d1mxfc_ C: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxfC00 C:11-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............----------.hhhhhhhhhhhhhhhhhhhhhhhhhhh.---------.eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxf C  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP----------KPIDAQVAELFGSNAVAPLFLIRAFARRQ---------NLSVVNLCDAmTDLPLPGFCVYTmAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAmPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -  |    130       140       150|        -|      170|      180   |   190       200       210       220|      230       240       250       260       270      
                                                                                                                               112        123                         151       161       171-MSE      184-MSE                              221-MSE                                                   


Chain D from PDB  Type:PROTEIN  Length:247
 aligned with Q8I814_TRYCR | Q8I814 from UniProtKB/TrEMBL  Length:276

    Alignment length:266
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
         Q8I814_TRYCR    11 CPAAIITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLPGDDTNGAAEAKPIDAQVAELFGSNAVAPLFLIRAFARRQGEGGAWRSRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADVIAFLVSKDAGYITGTTLKVDGGLILARA 276
               SCOP domains d1mxfd_ D: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxfD00 D:11-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -adh_short-1mxfD01 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -adh_short-1mxfD02 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -adh_short-1mxfD03 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -adh_short-1mxfD04 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeee....hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............----------.hhhhhhhhhhhhhhhhhhhhhhhhhhh.---------.eeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxf D  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP----------KPIDAQVAELFGSNAVAPLFLIRAFARRQ---------NLSVVNLCDAmTDLPLPGFCVYTmAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAmPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -  |    130       140       150|        -|      170|      180   |   190       200       210       220|      230       240       250       260       270      
                                                                                                                               112        123                         151       161       171-MSE      184-MSE                              221-MSE
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8I814_TRYCR | Q8I814)
molecular function
    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: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.
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.

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  1mxf
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 Related Entries

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

UniProtKB/TrEMBL
        Q8I814_TRYCR | Q8I814: 1mxh

(-) Related Entries Specified in the PDB File

1e7w CRYSTAL STRUCTURE OF LEISHMANIA MAJOR PTR1 (INHIBITOR COMPLEX)
1e92 CRYSTAL STRUCTURE OF LEISHMANIA MAJOR PTR1 (SUBSTRATE COMPLEX)