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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE FROM TRYPANOSOMA BRUCEI AT 1.8 A RESOLUTION
 
Authors :  J. Bosch, M. A. Robien, W. G. J. Hol, Structural Genomics Of Pathogen Protozoa Consortium (Sgpp)
Date :  16 Jun 05  (Deposition) - 26 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sgpp, Structural Genomics, Psi, Protein Structure Initiative, Nucleoside 2-Deoxyribosyltransferase, Structural Genomics Of Pathogenic Protozoa Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Bosch, M. A. Robien, C. Mehlin, E. Boni, A. Riechers, F. S. Buckner, W. C. Van Voorhis, P. J. Myler, E. A. Worthey, G. Detitta, J. R. Luft, A. Lauricella, S. Gulde, L. A. Anderson, O. Kalyuzhniy, H. M. Neely, J. Ross, T. N. Earnest, M. Soltis, L. Schoenfeld, F. Zucker, E. A. Merritt, E. Fan, C. L. Verlinde, W. G. J. Hol
Using Fragment Cocktail Crystallography To Assist Inhibitor Design Of Trypanosoma Brucei Nucleoside 2-Deoxyribosyltransferase.
J. Med. Chem. V. 49 5939 2006
PubMed-ID: 17004709  |  Reference-DOI: 10.1021/JM060429M

(-) Compounds

Molecule 1 - NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: T7 SYSTEM
    Gene: TB05.30H13.400
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE14Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:6 , HIS B:8 , MSE B:9 , LYS B:11 , ARG B:112 , ARG B:125 , HOH B:618BINDING SITE FOR RESIDUE SO4 B 461
2AC2SOFTWAREHIS A:6 , HIS A:8 , MSE A:9 , LYS A:11 , ARG A:112 , HOH A:568 , HOH A:642 , HOH A:651BINDING SITE FOR RESIDUE SO4 A 463
3AC3SOFTWAREALA A:15 , GLY A:16 , VAL A:19 , PHE A:20 , ASP A:84 , GLY A:86 , THR A:87 , GLU A:90 , HOH A:611 , ASN B:134BINDING SITE FOR RESIDUE GOL A 462
4AC4SOFTWAREASN A:134 , ALA B:15 , GLY B:16 , PHE B:20 , ASP B:84 , GLY B:86 , GLU B:90 , HOH B:558BINDING SITE FOR RESIDUE GOL B 464

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A0K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A0K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A0K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A0K)

(-) Exons   (0, 0)

(no "Exon" information available for 2A0K)

(-) 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:158
 aligned with Q57VC7_TRYB2 | Q57VC7 from UniProtKB/TrEMBL  Length:153

    Alignment length:158
                                  1                                                                                                                                                       
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144        
         Q57VC7_TRYB2     - ------MRKIYIAGPAVFNPDMGASYYNKVRELLKKENVMPLIPTDNEATGALDIRQKNIQMIKDCDAVIADLSPFRGHEPDCGTAFEVGYAAALNKMVLTFTSDRRNMREKYGSEVDKDNLRVEGFGLPFNLMLYDGVEVFDSFESAFKYFLANFPS 152
               SCOP domains ------d2a0ka1 A:9-160 Nucleoside 2-deoxyribosyltransferase                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeehhhhhh...hhhhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhh..eeeee.....hhhhhhh.................hhhhh.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a0k A   3 HHHHHHmRKIYIAGPAVFNPDmGASYYNKVRELLKKENVmPLIPTDNEATEALDIRQKNIQmIKDCDAVIADLSPFRGHEPDCGTAFEVGCAAALNKmVLTFTSDRRNmREKYGSGVDKDNLRVEGFGLPFNLmLYDGVEVFDSFESAFKYFLANFPS 160
                                  | 12        22 |      32        42        52        62 |      72        82        92       102       112       122       132   |   142       152        
                                  9-MSE         24-MSE            42-MSE                64-MSE                             100-MSE    111-MSE                  136-MSE                    


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with Q57VC7_TRYB2 | Q57VC7 from UniProtKB/TrEMBL  Length:153

    Alignment length:158
                                  1                                                                                                                                                       
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144        
         Q57VC7_TRYB2     - ------MRKIYIAGPAVFNPDMGASYYNKVRELLKKENVMPLIPTDNEATGALDIRQKNIQMIKDCDAVIADLSPFRGHEPDCGTAFEVGYAAALNKMVLTFTSDRRNMREKYGSEVDKDNLRVEGFGLPFNLMLYDGVEVFDSFESAFKYFLANFPS 152
               SCOP domains d2a0kb_ B: Nucleoside 2-deoxyribosyltransferase                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeehhhhhh...hhhhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhh..eeeee.....hhhhhhh.................hhhhh.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a0k B   3 HHHHHHmRKIYIAGPAVFNPDmGASYYNKVRELLKKENVmPLIPTDNEATEALDIRQKNIQmIKDCDAVIADLSPFRGHEPDCGTAFEVGCAAALNKmVLTFTSDRRNmREKYGSGVDKDNLRVEGFGLPFNLmLYDGVEVFDSFESAFKYFLANFPS 160
                                  | 12        22 |      32        42        52        62 |      72        82        92       102       112       122       132   |   142       152        
                                  9-MSE         24-MSE            42-MSE                64-MSE                             100-MSE    111-MSE                  136-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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A0K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A0K)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q57VC7_TRYB2 | Q57VC7)
molecular function
    GO:0070694    deoxyribonucleoside 5'-monophosphate N-glycosidase activity    Catalysis of the reaction: a deoxyribonucleoside 5'-monophosphate + H2O = deoxyribose 5-monophosphate + a purine or pyrimidine base.
    GO:0050144    nucleoside deoxyribosyltransferase activity    Catalysis of the reaction: 2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1.
biological process
    GO:0009159    deoxyribonucleoside monophosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.

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        Q57VC7_TRYB2 | Q57VC7: 2f2t 2f62 2f64 2f67

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