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- PDB-1adn: SOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1adn
TitleSOLUTION STRUCTURE OF THE DNA METHYLPHOSPHOTRIESTER REPAIR DOMAIN OF ESCHERICHIA COLI ADA
ComponentsN-ADA 10
KeywordsTRANSCRIPTION REGULATION
Function / homology
Function and homology information


: / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / DNA alkylation repair / methylation / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / positive regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
DNA Methylphosphotriester Repair Domain / DNA Methylphosphotriester Repair Domain / Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain ...DNA Methylphosphotriester Repair Domain / DNA Methylphosphotriester Repair Domain / Ada DNA repair, metal-binding / Bifunctional regulatory protein Ada / Ada-like domain superfamily / Metal binding domain of Ada / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Helix-turn-helix domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional transcriptional activator/DNA repair enzyme Ada
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsMyers, L.C. / Verdine, G.L. / Wagner, G.
Citation
Journal: Biochemistry / Year: 1993
Title: Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada.
Authors: Myers, L.C. / Verdine, G.L. / Wagner, G.
#1: Journal: Science / Year: 1993
Title: Repair of DNA Methylphosphotriesters Through a Metalloactivated Cysteine Nucleophile
Authors: Myers, L.C. / Terranova, M.P. / Ferentz, A.E. / Wagner, G. / Verdine, G.L.
History
DepositionSep 30, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: N-ADA 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5352
Polymers10,4701
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / -
Representative

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Components

#1: Protein N-ADA 10


Mass: 10469.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P06134
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR softwareName: DGII / Developer: HAVEL / Classification: refinement
RefinementSoftware ordinal: 1
Details: DATA WERE COLLECTED AT PH 6.4 AND AT 25 DEGREES CELSIUS. RESTRAINTS USED FOR THE STRUCTURE CALCULATIONS INCLUDED 547 NOE RESTRAINTS CONSISTING OF 108 INTRA-RESIDUE, 175 SEQUENTIAL, 91 MEDIUM (1<|I-J|<6) AND 173 LONG RANGE NOES. ADDITIONALLY, 50 HYDROGEN BONDING DISTANCES AS WELL AS DIHEDRAL ANGLE RESTRAINTS FOR 69 PHI ANGLES AND 8 CHI-1 ANGLES WERE INCLUDED. STEREOSPECIFIC ASSIGNMENTS HAVE BEEN MADE FOR THE METHYLENE PROTONS OF ASN 22, CYS 42, ASN 51, SER 53, PHE 54 AND TYR 55. STEREOSPECIFIC ASSIGNMENTS HAVE ALSO BEEN MADE FOR THE METHYL GROUPS OF VAL 16, LEU 17, VAL 28, LEU 48, VAL 52, LEU 62, AND LEU 84. THIS STUDY AND REFERENCE 1 ABOVE SHOW THAT CYS 38, CYS 42, CYS 69, AND CYS 72 ARE THE LIGANDS FOR A TIGHTLY BOUND ZINC ION. A 2.3 ANGSTROM THIOL - ZINC DISTANCE RESTRAINT WAS IMPOSED ON THE FOUR CYSTEINE METAL LIGANDS. ADDITIONAL DISTANCE AND DIHEDRAL RESTRAINTS WERE APPLIED TO ENFORCE A TETRAHEDRAL METAL LIGATION AND TO MAINTAIN PROPER SP3 HYBRIDIZATION GEOMETRIES OF THE COORDINATED SULFUR ATOMS. A DIHEDRAL ANGLE RESTRAINT MAINTAINS AN S TYPE LIGAND CONFIGURATION.
NMR ensembleConformers submitted total number: 14

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