3U80

1.60 Angstrom Resolution Crystal Structure of a 3-Dehydroquinate Dehydratase-like Protein from Bifidobacterium longum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of a type II dehydroquinate dehydratase-like protein from Bifidobacterium longum.

Light, S.H.Krishna, S.N.Bergan, R.C.Lavie, A.Anderson, W.F.

(2013) J Struct Funct Genomics 14: 25-30

  • DOI: 10.1007/s10969-013-9149-7
  • Primary Citation of Related Structures:  
    3U80

  • PubMed Abstract: 
  • Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. Here we identify a Bifidobacterium longum protein with high sequence homology to type II DHQDs but no detectable DHQD activity under standard assay conditions ...

    Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. Here we identify a Bifidobacterium longum protein with high sequence homology to type II DHQDs but no detectable DHQD activity under standard assay conditions. A crystal structure reveals that the B. longum protein adopts a DHQD-like tertiary structure but a distinct quaternary state. Apparently forming a dimer, the B. longum protein lacks the active site aspartic acid contributed from a neighboring protomer in the type II DHQD dodecamer. Relating to the absence of protein-protein interactions established in the type II DHQD dodecameric assembly, substantial conformational changes distinguish the would-be active site of the B. longum protein. As B. longum possess no other genes with homology to known DHQDs, these findings imply a unique DHQD activity within B. longum.


    Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases and Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-dehydroquinate dehydratase, type II AB151Bifidobacterium longum subsp. longum JDM301Mutation(s): 0 
Gene Names: BLJ_0876aroQ
EC: 4.2.1.10
Find proteins for D6ZTY6 (Bifidobacterium longum subsp. longum (strain JDM301))
Explore D6ZTY6 
Go to UniProtKB:  D6ZTY6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.004α = 90
b = 72.684β = 90
c = 81.713γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2013-05-08
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description