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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI DUTPASE IN COMPLEX WITH DUDP
 
Authors :  M. Harkiolaki, E. J. Dodson, V. Bernier-Villamor, J. P. Turkenburg, D. Gonzalez-Pacanowska, K. S. Wilson
Date :  07 May 03  (Deposition) - 22 Jan 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Dimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Harkiolaki, E. J. Dodson, V. Bernier-Villamor, J. P. Turkenburg, D. Gonzalez-Pacanowska, K. S. Wilson
The Crystal Structure Of Trypanosoma Cruzi Dutpase Reveals A Novel Dutp/Dudp Binding Fold
Structure V. 12 41 2004
PubMed-ID: 14725764  |  Reference-DOI: 10.1016/J.STR.2003.11.016

(-) Compounds

Molecule 1 - DEOXYURIDINE TRIPHOSPHATASE
    Chains: A, B, D, E
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-11C
    Expression System Vector Type: PLASMID
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 5693
    Strain: Y
    Synonym: DUTPASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1DUD3Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1DUD1Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1DUD2Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:60 , TRP A:61 , TRP A:62 , GLN B:22 , LEU B:25 , ASN B:26 , MET B:29 , TRP B:42 , GLU B:49 , GLU B:52 , GLU B:77 , ASP B:80 , HIS B:83 , PHE B:84 , LYS B:197 , ASN B:201 , ARG B:204 , TYR B:209 , LYS B:216 , ASN B:224BINDING SITE FOR RESIDUE DUD B1280
2AC2SOFTWAREGLN D:22 , LEU D:25 , ASN D:26 , MET D:29 , TRP D:42 , GLU D:49 , GLU D:52 , ASP D:80 , HIS D:83 , PHE D:84 , LYS D:197 , ASN D:201 , ARG D:204 , TYR D:209 , LYS D:216 , ASN D:224 , LYS E:60 , TRP E:61 , TRP E:62BINDING SITE FOR RESIDUE DUD D1280
3AC3SOFTWARELYS D:60 , TRP D:61 , TRP D:62 , GLN E:22 , LEU E:25 , ASN E:26 , TRP E:42 , GLU E:49 , GLU E:52 , GLU E:77 , ASP E:80 , HIS E:83 , PHE E:84 , LYS E:197 , ASN E:201 , ARG E:204 , TYR E:209 , LYS E:216 , ASN E:224BINDING SITE FOR RESIDUE DUD E1281

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:148 -Pro A:149
2Phe B:148 -Pro B:149
3Phe D:148 -Pro D:149
4Phe E:148 -Pro E:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OGK)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:230
 aligned with O15923_TRYCR | O15923 from UniProtKB/TrEMBL  Length:283

    Alignment length:271
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279 
         O15923_TRYCR    10 VPARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKRTQDEKGADDVALKSLKEMGFFCRPPAHAKSTAASGQRTNGGDGDGDDELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQLKGYKEGVYVKVREGVEDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAALD 280
               SCOP domains d1ogka_ A: Type II deoxyuridine triphosphatase                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh.-------..hhhhhhhhh........-------------------hhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh---------------hhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogk A  10 VPARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKR-------DDVALKSLKEMGFFCRPPA-------------------DDELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQL---------------EDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAALD 280
                                    19        29        39        49        59        69        79        89   |     - |     109       119         -       139       149       159       169       179       189       199      |  -         -  |    229       239       249       259       269       279 
                                                                                                              93     101               119                 139                                                                206             222                                                          


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with O15923_TRYCR | O15923 from UniProtKB/TrEMBL  Length:283

    Alignment length:269
                                    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         
         O15923_TRYCR    11 PARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKRTQDEKGADDVALKSLKEMGFFCRPPAHAKSTAASGQRTNGGDGDGDDELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQLKGYKEGVYVKVREGVEDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAAL 279
               SCOP domains d1ogkb_ B: Type II deoxyuridine triphosphatase                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh.--------hhhhhhhhhhh......---------------------............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.........ee..eehhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogk B  11 PARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKR--------DVALKSLKEMGFFCRPP---------------------DELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQLKGYKEGVYVKVREGVEDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAAL 279
                                    20        30        40        50        60        70        80        90  |      - |     110       | -         -       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
                                                                                                             93      102             118                   140                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with O15923_TRYCR | O15923 from UniProtKB/TrEMBL  Length:283

    Alignment length:269
                                    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         
         O15923_TRYCR    11 PARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKRTQDEKGADDVALKSLKEMGFFCRPPAHAKSTAASGQRTNGGDGDGDDELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQLKGYKEGVYVKVREGVEDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAAL 279
               SCOP domains d1ogkd_ D: Type II deoxyuridine triphosphatase                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh...----------...hhhhhh......---------------------hhhhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogk D  11 PARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKR----------ALKSLKEMGFFCRPP---------------------DELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQLKGYKEGVYVKVREGVEDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAAL 279
                                    20        30        40        50        60        70        80        90  |      -   |   110       | -         -       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
                                                                                                             93        104           118                   140                                                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:242
 aligned with O15923_TRYCR | O15923 from UniProtKB/TrEMBL  Length:283

    Alignment length:271
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279 
         O15923_TRYCR    10 VPARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKRTQDEKGADDVALKSLKEMGFFCRPPAHAKSTAASGQRTNGGDGDGDDELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQLKGYKEGVYVKVREGVEDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAALD 280
               SCOP domains d1ogke_ E: Type II deoxyuridine triphosphatase                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----dUTPase_2-1ogkE01 E:14-209                                                                                                                                                                          ----------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----dUTPase_2-1ogkE02 E:14-209                                                                                                                                                                          ----------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----dUTPase_2-1ogkE03 E:14-209                                                                                                                                                                          ----------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----dUTPase_2-1ogkE04 E:14-209                                                                                                                                                                          ----------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.--------hhhhhhhhhhh......---------------------............hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee...hhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ogk E  10 VPARVLNSLAHLQDGLNIFMDPDWRQIRHVDDWALAITMESAELIDSYPWKWWKNVKAQTDMHNVRIEIADILHFSLSGEIQKR--------DVALKSLKEMGFFCRPP---------------------DELLELMFFPLTEVASAVATFRNIIQLASIYRFDLITKGLLLAAQDLDFNLVGYYVAKYTLNQIRQLKGYKEGVYVKVREGVEDNELLHECVQSVSVEDVLNEGTYLKAWEKIACSVFDAFGMPEEERRHAYDWLKSAALD 280
                                    19        29        39        49        59        69        79        89   |     -  |    109        |-         -         -|      149       159       169       179       189       199       209       219       229       239       249       259       269       279 
                                                                                                              93      102             118                   140
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1OGK)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: MazG (25)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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

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        O15923_TRYCR | O15923: 1ogl

(-) Related Entries Specified in the PDB File

1ogl THE CRYSTAL STRUCTURE OF NATIVE TRYPANOSOMA CRUZI DUTPASE