1RWU

Solution structure of conserved protein YbeD from E. coli


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.3 of the entry. See complete history


Literature

Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains

Kozlov, G.Elias, D.Semesi, A.Yee, A.Cygler, M.Gehring, K.

(2004) J Bacteriol 186: 8083-8088

  • DOI: 10.1128/JB.186.23.8083-8088.2004
  • Primary Citation of Related Structures:  
    1RWU

  • PubMed Abstract: 
  • Lipoic acid is an essential prosthetic group in several metabolic pathways. The biosynthetic pathway of protein lipoylation in Escherichia coli involves gene products of the lip operon. YbeD is a conserved bacterial protein located in the dacA-lipB intergenic region ...

    Lipoic acid is an essential prosthetic group in several metabolic pathways. The biosynthetic pathway of protein lipoylation in Escherichia coli involves gene products of the lip operon. YbeD is a conserved bacterial protein located in the dacA-lipB intergenic region. Here, we report the nuclear magnetic resonance structure of YbeD from E. coli. The structure includes a beta alpha beta beta alpha beta fold with two alpha-helices on one side of a four-strand antiparallel beta-sheet. The beta 2-beta 3 loop shows the highest sequence conservation and is likely functionally important. The beta-sheet surface contains a patch of conserved hydrophobic residues, suggesting a role in protein-protein interactions. YbeD shows striking structural homology to the regulatory domain from d-3-phosphoglycerate dehydrogenase, hinting at a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical UPF0250 protein ybeDA109Escherichia coliMutation(s): 0 
Gene Names: ybeDb0631C0721Z0776ECS0669SF0650S0672
UniProt
Find proteins for P0A8J4 (Escherichia coli (strain K12))
Explore P0A8J4 
Go to UniProtKB:  P0A8J4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8J4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 1RWU Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations