1RES

DETERMINATION OF THE STRUCTURE OF THE DNA BINDING DOMAIN OF GAMMA DELTA RESOLVASE IN SOLUTION


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Determination of the structure of the DNA binding domain of gamma delta resolvase in solution.

Liu, T.DeRose, E.F.Mullen, G.P.

(1994) Protein Sci 3: 1286-1295

  • DOI: 10.1002/pro.5560030815
  • Primary Citation of Related Structures:  
    1RES, 1RET

  • PubMed Abstract: 
  • The DNA binding domain (DBD) of gamma delta resolvase (residues 141-183) is responsible for the interaction of this site-specific DNA recombinase with consensus site DNA within the gamma delta transposable element in Escherichia coli. Based on chemical-shift comparisons, the proteolytically isolated DBD displays side-chain interactions within a hydrophobic core that are highly similar to those of this domain when part of the intact enzyme (Liu T, Liu DJ, DeRose EF, Mullen GP, 1993, J Biol Chem 268:16309-16315) ...

    The DNA binding domain (DBD) of gamma delta resolvase (residues 141-183) is responsible for the interaction of this site-specific DNA recombinase with consensus site DNA within the gamma delta transposable element in Escherichia coli. Based on chemical-shift comparisons, the proteolytically isolated DBD displays side-chain interactions within a hydrophobic core that are highly similar to those of this domain when part of the intact enzyme (Liu T, Liu DJ, DeRose EF, Mullen GP, 1993, J Biol Chem 268:16309-16315). The structure of the DBD in solution has been determined using restraints obtained from 2-dimensional proton NMR data and is represented by 17 conformers. Experimental restraints included 458 distances based on analysis of nuclear Overhauser effect connectivities, 17 phi and chi 1 torsion angles based on analysis of couplings, and 17 backbone hydrogen bonds determined from NH exchange data. With respect to the computed average structure, these conformers display an RMS deviation of 0.67 A for the heavy backbone atoms and 1.49 A for all heavy atoms within residues 149-180. The DBD consists of 3 alpha-helices comprising residues D149-Q157, S162-T167, and R172-N183. Helix-2 and helix-3 form a backbone fold, which is similar to the canonical helix-turn-helix motif. The conformation of the NH2-terminal residues, G141-R148, appears flexible in solution. A hydrophobic core is formed by side chains donated by essentially all hydrophobic residues within the helices and turns. Helix-1 and helix-3 cross with a right-handed folding topology. The structure is consistent with a mechanism of DNA binding in which contacts are made by the hydrophilic face of helix-3 in the major groove and the amino-terminal arm in the minor groove. This structure represents an important step toward analysis of the mechanism of DNA interaction by gamma delta resolvase and provides initial structure-function comparisons among the divergent DBDs of related resolvases and invertases.


    Organizational Affiliation

    Department of Chemistry, University of Wisconsin at Milwaukee 53211.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GAMMA DELTA-RESOLVASEA43Escherichia coliMutation(s): 0 
UniProt
Find proteins for P03012 (Escherichia coli (strain K12))
Explore P03012 
Go to UniProtKB:  P03012
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UniProt GroupP03012
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • OLDERADO: 1RES Olderado

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1994-06-29 
  • Released Date: 1994-11-30 
  • Deposition Author(s): Mullen, G.P.

Revision History  (Full details and data files)

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations, Other