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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS OGT IN COMPLEX WITH DNA
 
Authors :  R. Miggiano, F. Rossi, S. Garavaglia, M. Rizzi
Date :  13 Nov 14  (Deposition) - 04 Nov 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 2:  A (1x),B (1x),C (1x),D (1x),E (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x),E (1x)
Keywords :  Direct Dna Damage Reversal, Alkylated Dna-Protein Alkyltransferase, Protein-Dna Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Miggiano, G. Perugino, M. Ciaramella, M. Serpe, D. Rejman, O. Pav, R. Pohl, S. Garavaglia, S. Lahiri, M. Rizzi, F. Rossi
Crystal Structure Of Mycobacterium Tuberculosis O6-Methylguanine-Dna Methyltransferase Protein Clusters Assembled On To Damaged Dna.
Biochem. J. V. 473 123 2016
PubMed-ID: 26512127  |  Reference-DOI: 10.1042/BJ20150833

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.1.1.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: OGT, RV1316C, MTCY130.01C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: 6-O-METHYLGUANINE-DNA METHYLTRANSFERASE,MGMT,O-6- METHYLGUANINE-DNA-ALKYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)
Biological Unit 2 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)E (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1E1X1Mod. NucleotidePHOSPHORIC ACID MONO-[5-(1-ETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-PURIN-9-YL)-3-HYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]ESTER
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1E1X1Mod. NucleotidePHOSPHORIC ACID MONO-[5-(1-ETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-PURIN-9-YL)-3-HYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]ESTER
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1E1X-1Mod. NucleotidePHOSPHORIC ACID MONO-[5-(1-ETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-PURIN-9-YL)-3-HYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]ESTER
2GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1E1X-1Mod. NucleotidePHOSPHORIC ACID MONO-[5-(1-ETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-PURIN-9-YL)-3-HYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]ESTER
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:65 , ASP A:66 , VAL A:67 , LEU A:69 , LEU A:85binding site for residue GOL A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WX9)

(-) Exons   (0, 0)

(no "Exon" information available for 4WX9)

(-) 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:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeee..eeeeeee.........ee....hhhhhhhhhhhhhh.......ee....hhhhhhhhhhhh.......eehhhhhhhh....hhhhhhhhhhh.......hhh.ee...........hhhhhhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wx9 A   2 VHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD 165
                                    11        21        31||      44        54        64        74        84        94       104       114       124       134       144       154       164 
                                                         32|                                                                                                                                 
                                                          36                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeee..eeeeeee............ee....hhhhhhhhhhhhh..............hhhhhhhhhhhhhh.....eehhhhhhhh......hhhhhhhhh.......hhh.ee...........hhhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wx9 B   2 VHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTYEPSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    


Chain C from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeeee..eeeeee.............ee....hhhhhhhhhhhhh..............hhhhhhhhhhhh.......eehhhhhhhh....hhhhhhhhhhh.......hhh.ee...........hhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wx9 C   2 VHYRTIDSPIGPLTLAGHGSVLTNLRMLEQTYEPSRTHWTPDPGAFSGAVDQLNAYFAGELTEFDVELDLRGTDFQQRVWKALLTIPYGETRSYGEIADQIGAPGAARAVGLANGHNPIAIIVPCHRVIGASGKLTGYGGGINRKRALLELEKSRAPADLTLFD 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    


Chain D from PDB  Type:DNA  Length:13
                                             
                 4wx9 D   1 GCCATGxCTAGTA  13
                                  | 10   
                                  7-E1X  


Chain E from PDB  Type:DNA  Length:13
                                             
                 4wx9 E  14 TACTAGCCATGGC  26
                                    23
   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  (0, 0)

(no "SCOP Domain" information available for 4WX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WX9)

(-) Gene Ontology  (12, 12)

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  4wx9
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        OGT_MYCTU | P9WJW5: 4bhb 4bhc 4wxc 4wxd

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