5Z6V

Crystal structure of a substrate-binding protein from Rhodothermus marinus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Literature

Crystal structure of a substrate-binding protein from Rhodothermus marinus reveals a single alpha / beta-domain.

Bae, J.E.Kim, I.J.Kim, K.J.Nam, K.H.

(2018) Biochem Biophys Res Commun 497: 368-373

  • DOI: 10.1016/j.bbrc.2018.02.086
  • Primary Citation of Related Structures:  
    5Z6V

  • PubMed Abstract: 
  • Substrate-binding proteins (SBPs) bind to specific ligands and are associated with membrane protein complexes for transport or signal transduction. Most SBPs recognize substrates by the hinge motion between two distinct α/β domains. However, short SBP motifs are often observed in protein databases, which are located around methyl-accepting chemotaxis protein genes, but structural and functional studies have yet to be performed ...

    Substrate-binding proteins (SBPs) bind to specific ligands and are associated with membrane protein complexes for transport or signal transduction. Most SBPs recognize substrates by the hinge motion between two distinct α/β domains. However, short SBP motifs are often observed in protein databases, which are located around methyl-accepting chemotaxis protein genes, but structural and functional studies have yet to be performed. Here, we report the crystal structure of an unusually small SBP from Rhodothermus marinus (named as RmSBP) at 1.9 Å. This protein is composed of a single α/β-domain, unlike general SBPs that have two distinct domains. RmSBP exhibits a high structural similarity to the C-terminal domain of the previously reported amino acid bound SBPs, while it does not contain an N-terminal domain for substrate recognition. As a result of the structural comparison analysis, RmSBP has a putative SBP that is different from the previously reported SBP. Our results provide insight into a new class of substrate recognition mechanism by the mini SBP protein.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Republic of Korea. Electronic address: structure@postech.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ABC-type uncharacterized transport system periplasmic component-like proteinA189Rhodothermus marinus DSM 4252Mutation(s): 0 
Gene Names: Rmar_2176
UniProt
Find proteins for D0MDR1 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MDR1 
Go to UniProtKB:  D0MDR1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0MDR1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.9α = 90
b = 63.32β = 97.22
c = 34.666γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2017R1D1A1B03033087
National Research Foundation (Korea)Korea, Republic Of2017M3A9F6029736

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release