6SVF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

Starting Model: experimental
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This is version 1.1 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 F Struct Biol Commun 75: 707-713

  • DOI: https://doi.org/10.1107/S2053230X1901464X
  • Primary Citation of Related Structures:  
    6SVF

  • 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 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 has 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amino acid ABC transporter, periplasmic amino acid-binding protein229Thermotoga maritima MSB8Mutation(s): 1 
Gene Names: TM_0593
UniProt
Find proteins for Q9WZ62 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZ62 
Go to UniProtKB:  Q9WZ62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZ62
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ARG
Query on ARG

Download Ideal Coordinates CCD File 
B [auth A]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.72α = 90
b = 52.964β = 90
c = 95.686γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
EVAL15data reduction
EVAL15data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description