General Information

Database accession: MF2140001

Name: Arc repressor

PDB ID: 1arq PDB

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 PubMed

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.


Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GeneOntology

Biological process:

transcription, DNA-templated The cellular synthesis of RNA on a template of DNA. GeneOntology

regulation of transcription, DNA-templated Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GeneOntology

Cellular component: not assigned

Structure Summary Structural annotations of the participating protein chains.

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


Chain A

Name: Transcriptional repressor arc

Source organism: Enterobacteria phage P22

Length: 53 residues

Sequence:Sequence according to PDB SEQRESMKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA

UniProtKB AC: P03050 (positions: 1-53) UniProt Coverage: 100%

UniRef90 AC: UniRef90_P03050 (positions: 1-53) UniRef90

Chain B

Name: Transcriptional repressor arc

Source organism: Enterobacteria phage P22

Length: 53 residues

Sequence:Sequence according to PDB SEQRESMKGMSKMPQFNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIGA

UniProtKB AC: P03050 (positions: 1-53) UniProt Coverage: 100%

UniRef90 AC: UniRef90_P03050 (positions: 1-53) UniRef90

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

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).

Related Structure(s) Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap).

There are 10 related structures in the Protein Data Bank:





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