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(-) Description

Title :  CRYSTAL STRUCTURE OF SUBSTRATE 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 :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sdr Topology, Protein-Substrate 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: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1DHF4Ligand/IonDIHYDROFOLIC ACID
2NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:22 , ILE A:23 , TYR A:42 , ARG A:43 , HIS A:44 , SER A:45 , 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 , DHF A:1278 , HOH A:1302 , HOH A:1318BINDING SITE FOR RESIDUE NAP A 1277
2AC2SOFTWAREARG A:22 , SER A:103 , TYR A:105 , PRO A:107 , ASP A:169 , PHE A:179 , TYR A:182 , PRO A:218 , MET A:221 , TYR A:229 , NAP A:1277 , HOH A:1299 , HOH A:1372BINDING SITE FOR RESIDUE DHF A 1278
3AC3SOFTWAREARG B:21 , ARG 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 , GLU B:131 , LEU B:167 , CYS B:168 , TYR B:182 , LYS B:186 , PRO B:212 , GLY B:213 , SER B:215 , LEU B:216 , DHF B:2278 , HOH B:2295 , HOH B:2366BINDING SITE FOR RESIDUE NAP B 2277
4AC4SOFTWAREARG B:22 , SER B:103 , TYR B:105 , PRO B:107 , ASP B:169 , PHE B:179 , TYR B:182 , PRO B:218 , MET B:221 , TYR B:229 , NAP B:2277 , HOH B:2321 , HOH B:2352BINDING SITE FOR RESIDUE DHF B 2278
5AC5SOFTWAREARG C:21 , ARG C:22 , ILE C:23 , TYR C:42 , 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 , ALA C:104 , LEU C:167 , CYS C:168 , TYR C:182 , LYS C:186 , PRO C:212 , GLY C:213 , SER C:215 , LEU C:216 , DHF C:3278 , HOH C:3280 , HOH C:3292 , HOH C:3342BINDING SITE FOR RESIDUE NAP C 3277
6AC6SOFTWAREARG C:22 , SER C:103 , TYR C:105 , PRO C:107 , ASP C:169 , PHE C:179 , TYR C:182 , PRO C:218 , MET C:221 , TYR C:229 , NAP C:3277 , HOH C:3298 , HOH C:3345 , HOH C:3386BINDING SITE FOR RESIDUE DHF 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 , ALA D:104 , 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 , DHF D:4278 , HOH D:4288 , HOH D:4291 , HOH D:4302 , HOH D:4312 , HOH D:4350 , HOH D:4352 , HOH D:4380BINDING SITE FOR RESIDUE NAP D 4277
8AC8SOFTWAREARG D:22 , SER D:103 , TYR D:105 , PRO D:107 , ASP D:169 , PHE D:179 , TYR D:182 , PRO D:218 , MET D:221 , TYR D:229 , NAP D:4277 , HOH D:4348 , HOH D:4350 , HOH D:4388BINDING SITE FOR RESIDUE DHF D 4278

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MXH)

(-) 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:248
 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 d1mxha_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxhA00 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....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxh A  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP-----------PIDAQVAELFGSNAVAPLFLIRAFARRQ-------SRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -   |   130       140       150|      160       170       180       190       200       210       220       230       240       250       260       270      
                                                                                                                               112         124                        151     159                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:248
 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 d1mxhb_ B: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxhB00 B: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...........hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxh B  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP-----------PIDAQVAELFGSNAVAPLFLIRAFARRQ-------SRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -   |   130       140       150|      160       170       180       190       200       210       220       230       240       250       260       270      
                                                                                                                               112         124                        151     159                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:248
 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 d1mxhc_ C: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxhC00 C: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....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxh C  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP-----------PIDAQVAELFGSNAVAPLFLIRAFARRQ-------SRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -   |   130       140       150|      160       170       180       190       200       210       220       230       240       250       260       270      
                                                                                                                               112         124                        151     159                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:248
 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 d1mxhd_ D: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                 SCOP domains
               CATH domains 1mxhD00 D:11-276 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                       CATH domains
           Pfam domains (1) -adh_short-1mxhD01 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -adh_short-1mxhD02 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -adh_short-1mxhD03 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -adh_short-1mxhD04 D:12-201                                                                                                                                                                    --------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............-----------hhhhhhhhhhhhhhhhhhhhhhhhhhh.-------....eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mxh D  11 CPAAVITGGARRIGHSIAVRLHQQGFRVVVHYRHSEGAAQRLVAELNAARAGSAVLCKGDLSLSSSLLDCCEDIIDCSFRAFGRCDVLVNNASAYYPTPLLP-----------PIDAQVAELFGSNAVAPLFLIRAFARRQ-------SRNLSVVNLCDAMTDLPLPGFCVYTMAKHALGGLTRAAALELAPRHIRVNAVAPGLSLLPPAMPQETQEEYRRKVPLGQSEASAAQIADAIAFLVSKDAGYITGTTLKVDGGLILARA 276
                                    20        30        40        50        60        70        80        90       100       110 |       -   |   130       140       150|      160       170       180       190       200       210       220       230       240       250       260       270      
                                                                                                                               112         124                        151     159
   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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  1mxh
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 Related Entries

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

UniProtKB/TrEMBL
        Q8I814_TRYCR | Q8I814: 1mxf

(-) 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)
1mxf CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI PTR2 (INHIBITOR COMPLEX)