6SVF

Crystal structure of the P235GK mutant of ArgBP from T. maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The non-swapped monomeric structure of the arginine-binding protein from Thermotoga maritima.

Smaldone, G.Ruggiero, A.Balasco, N.Abuhammad, A.Autiero, I.Caruso, D.Esposito, D.Ferraro, G.Gelardi, E.L.M.Moreira, M.Quareshy, M.Romano, M.Saaret, A.Selvam, I.Squeglia, F.Troisi, R.Kroon-Batenburg, L.M.J.Esposito, L.Berisio, R.Vitagliano, L.

(2019) Acta Crystallogr.,Sect.F 75: 707-713

  • DOI: 10.1107/S2053230X1901464X

  • PubMed Abstract: 
  • Domain swapping is a widespread oligomerization process that is observed in a large variety of protein families. In the large superfamily of substrate-binding proteins, non-monomeric members have rarely been reported. The arginine-binding protein fro ...

    Domain swapping is a widespread oligomerization process that is observed in a large variety of protein families. In the large superfamily of substrate-binding proteins, non-monomeric members have rarely been reported. The arginine-binding protein from Thermotoga maritima (TmArgBP), a protein endowed with a number of unusual properties, presents a domain-swapped structure in its dimeric native state in which the two polypeptide chains mutually exchange their C-terminal helices. It has previously been shown that mutations in the region connecting the last two helices of the TmArgBP structure lead to the formation of a variety of oligomeric states (monomers, dimers, trimers and larger aggregates). With the aim of defining the structural determinants of domain swapping in TmArgBP, the monomeric form of the P235GK mutant hasĀ been structurally characterized. Analysis of this arginine-bound structure indicates that it consists of a closed monomer with its C-terminal helix folded against the rest of the protein, as typically observed for substrate-binding proteins. Notably, the two terminal helices are joined by a single nonhelical residue (Gly235). Collectively, the present findings indicate that extending the hinge region and conferring it with more conformational freedom makes the formation of a closed TmArgBP monomer possible. On the other hand, the short connection between the helices may explain the tendency of the protein to also adopt alternative oligomeric states (dimers, trimers and larger aggregates). The data reported here highlight the importance of evolutionary control to avoid the uncontrolled formation of heterogeneous and potentially harmful oligomeric species through domain swapping.


    Organizational Affiliation

    AIC School Crystallographic Information Fiesta 2019, Naples, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Amino acid ABC transporter, periplasmic amino acid-binding protein
A
229Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 1 
Find proteins for Q9WZ62 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WZ62
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.720α = 90.00
b = 52.964β = 90.00
c = 95.686γ = 90.00
Software Package:
Software NamePurpose
EVAL15data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
EVAL15data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-20
    Type: Initial release