Database accession: MF2140001
Name: Arc repressor
PDB ID: 1arq
Experimental method: NMR
Assembly: homodimer
Source organism: Enterobacteria phage P22
Primer publication of the structure:
Bonvin AM, Vis H, Breg JN, Burgering MJ, Boelens R, Kaptein R
Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations.
(1994) J. Mol. Biol. 236: 328-41
PMID: 8107113
Abstract:
The Arc repressor of Salmonella bacteriophage P22 is a dimeric sequence-specific DNA-binding protein. The solution structure of Arc has been determined from 2D NMR data using an "ensemble" iterative relaxation matrix approach (IRMA) followed by direct NOE refinement with DINOSAUR. A set of 51 structures was generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-ups in H2O and 2H2O via relaxation matrix calculations from the ensemble of structures. Methyl group rotation, aromatic ring flaps and internal mobility effects (via order parameters obtained from a free molecular dynamics run in water) were included in these calculations. The best structures were finally refined with direct NOE constraints following a slow-cooling simulated annealing protocol. In this final refinement stage, theoretical NOE intensities were directly compared with the experimental data and forces were derived using a simple two-spin approximation for the gradient of the NOE function. Dynamic assignment was applied to the peaks involving unassigned diastereotopic groups. The structure is determined to a precision (r.m.s.d. from the average excluding the ill defined C and N-terminal region) of 0.55 and 1.10 A for backbone and all atoms, respectively. The final structures, with R factor values around 0.35, have good stereochemical qualities, contain an extensive network of hydrogen bonds consistent with the secondary structure elements and structural features in concordance with genetic data. The overall folding of the solution and crystal structures is the same.
Molecular function:
Biological process:
transcription, DNA-templated The cellular synthesis of RNA on a template of DNA.
regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
Cellular component: not assigned
Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: No modifications of the original PDB file. Chain identifiers are identical with the PDB's identifiers.
Number of unique protein segments: 1
Name: Transcriptional repressor arc
Source organism: Enterobacteria phage P22
Length: 53 residues
Sequence:Sequence according to PDB SEQRESMKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA
UniProtKB AC: P03050 (positions: 1-53)
Coverage: 100%UniRef90 AC: UniRef90_P03050 (positions: 1-53)
Name: Transcriptional repressor arc
Source organism: Enterobacteria phage P22
Length: 53 residues
Sequence:Sequence according to PDB SEQRESMKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA
UniProtKB AC: P03050 (positions: 1-53)
Coverage: 100%UniRef90 AC: UniRef90_P03050 (positions: 1-53)
Complex evidence:
The Arc repressor protein has been experimentally shown to be a molten globule in monomeric form (PMID: 8446590, PMID: 7696567). Adopting the proper three dimensional structure is linked to dimerization (PMID: 8110744, PMID: 10889040).