3NCV

NgoL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer

Namadurai, S.Jain, D.Kulkarni, D.S.Tabib, C.R.Friedhoff, P.Rao, D.N.Nair, D.T.

(2010) Plos One 5: e13726-e13726

  • DOI: 10.1371/journal.pone.0013726

  • PubMed Abstract: 
  • The mismatch repair (MMR) pathway serves to maintain the integrity of the genome by removing mispaired bases from the newly synthesized strand. In E. coli, MutS, MutL and MutH coordinate to discriminate the daughter strand through a mechanism involvi ...

    The mismatch repair (MMR) pathway serves to maintain the integrity of the genome by removing mispaired bases from the newly synthesized strand. In E. coli, MutS, MutL and MutH coordinate to discriminate the daughter strand through a mechanism involving lack of methylation on the new strand. This facilitates the creation of a nick by MutH in the daughter strand to initiate mismatch repair. Many bacteria and eukaryotes, including humans, do not possess a homolog of MutH. Although the exact strategy for strand discrimination in these organisms is yet to be ascertained, the required nicking endonuclease activity is resident in the C-terminal domain of MutL. This activity is dependent on the integrity of a conserved metal binding motif. Unlike their eukaryotic counterparts, MutL in bacteria like Neisseria exist in the form of a homodimer. Even though this homodimer would possess two active sites, it still acts a nicking endonuclease. Here, we present the crystal structure of the C-terminal domain (CTD) of the MutL homolog of Neisseria gonorrhoeae (NgoL) determined to a resolution of 2.4 Å. The structure shows that the metal binding motif exists in a helical configuration and that four of the six conserved motifs in the MutL family, including the metal binding site, localize together to form a composite active site. NgoL-CTD exists in the form of an elongated inverted homodimer stabilized by a hydrophobic interface rich in leucines. The inverted arrangement places the two composite active sites in each subunit on opposite lateral sides of the homodimer. Such an arrangement raises the possibility that one of the active sites is occluded due to interaction of NgoL with other protein factors involved in MMR. The presentation of only one active site to substrate DNA will ensure that nicking of only one strand occurs to prevent inadvertent and deleterious double stranded cleavage.


    Organizational Affiliation

    Laboratory 4, National Centre for Biological Sciences, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA mismatch repair protein mutL
A, B
220Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)Mutation(s): 0 
Gene Names: mutL
Find proteins for Q5F8M6 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Go to UniProtKB:  Q5F8M6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.500α = 90.00
b = 62.100β = 104.60
c = 92.100γ = 90.00
Software Package:
Software NamePurpose
SHELXSphasing
HKL-2000data scaling
MxCuBEdata collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance