PDBsum entry 4kyc

Binding protein, viral protein

PDB id: 4kyc

Contents

Protein chain

420 a.a.

Ligands

GLC-GLC

EDO

BO3

Waters ×306

PDB id:

4kyc

Name:

Binding protein, viral protein

Title:

Structure of thE C-terminal domain of the menangle virus phosphoprotein, fused to mbp.

Structure:

Maltose-binding periplasmic protein, phosphoprotein, chimeric construct. Chain: a. Fragment: unprot p0aex9 residues 27-392, unprot q91mk1 residues 339- 388. Synonym: mbp, mmbp, maltodextrin-binding protein. Engineered: yes. Mutation: yes

Source:

Escherichia coli, menangle virus. Organism_taxid: 83333, 152219. Strain: k12, unnamed isolate. Gene: b4034, jw3994, male, p, v/p. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.95Å R-factor: 0.186 R-free: 0.213

Authors:

K.Yegambaram,E.M.M.Bulloch,R.L.Kingston

Key ref:

K.Yegambaram et al. (2013). Protein domain definition should allow for conditional disorder. Protein Sci, 22, 1502-1518. PubMed id: 23963781 DOI: 10.1002/pro.2336

Date:

28-May-13 Release date: 25-Sep-13

Protein chain

P0AEX9  (MALE_ECOLI) -  Maltose/maltodextrin-binding periplasmic protein from Escherichia coli (strain K12)

Seq: 396 a.a.

Struc: 420 a.a.*

Protein chain

Q91MK1  (Q91MK1_9MONO) -  Phosphoprotein from Menangle virus

Seq: 388 a.a.

Struc: 420 a.a.*

* PDB and UniProt seqs differ at 294 residue positions (black crosses)

DOI no: 10.1002/pro.2336

Protein Sci 22:1502-1518 (2013)

PubMed id: 23963781

Protein domain definition should allow for conditional disorder.

K.Yegambaram, E.M.Bulloch, R.L.Kingston.

ABSTRACT

Proteins are often classified in a binary fashion as either structured or disordered. However this approach has several deficits. Firstly, protein folding is always conditional on the physiochemical environment. A protein which is structured in some circumstances will be disordered in others. Secondly, it hides a fundamental asymmetry in behavior. While all structured proteins can be unfolded through a change in environment, not all disordered proteins have the capacity for folding. Failure to accommodate these complexities confuses the definition of both protein structural domains and intrinsically disordered regions. We illustrate these points with an experimental study of a family of small binding domains, drawn from the RNA polymerase of mumps virus and its closest relatives. Assessed at face value the domains fall on a structural continuum, with folded, partially folded, and near unstructured members. Yet the disorder present in the family is conditional, and these closely related polypeptides can access the same folded state under appropriate conditions. Any heuristic definition of the protein domain emphasizing conformational stability divides this domain family in two, in a way that makes no biological sense. Structural domains would be better defined by their ability to adopt a specific tertiary structure: a structure that may or may not be realized, dependent on the circumstances. This explicitly allows for the conditional nature of protein folding, and more clearly demarcates structural domains from intrinsically disordered regions that may function without folding.