Crystal Structure of the E. coli adaptive response protein AidB in the space group P3(2)

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Flavin-induced oligomerization in Escherichia coli adaptive response protein AidB.

Hamill, M.J.Jost, M.Wong, C.Elliott, S.J.Drennan, C.L.

(2011) Biochemistry 50: 10159-10169

  • DOI: https://doi.org/10.1021/bi201340t
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The process known as "adaptive response" allows Escherichia coli to respond to small doses of DNA-methylating agents by upregulating the expression of four proteins. While the role of three of these proteins in mitigating DNA damage is well understood, the function of AidB is less clear. Although AidB is a flavoprotein, no catalytic role has been established for the bound cofactor. Here we investigate the possibility that flavin plays a structural role in the assembly of the AidB tetramer. We report the generation and biophysical characterization of deflavinated AidB and of an AidB mutant that has greatly reduced affinity for flavin adenine dinucleotide (FAD). Using fluorescence quenching and analytical ultracentrifugation, we find that apo AidB has a high affinity for FAD, as indicated by an apparent dissociation constant of 402.1 ± 35.1 nM, and that binding of substoichiometric amounts of FAD triggers a transition in the AidB oligomeric state. In particular, deflavinated AidB is dimeric, whereas the addition of FAD yields a tetramer. We further investigate the dimerization and tetramerization interfaces of AidB by determining a 2.8 Å resolution crystal structure in space group P3(2) that contains three intact tetramers in the asymmetric unit. Taken together, our findings provide strong evidence that FAD plays a structural role in the formation of tetrameric AidB.

  • Organizational Affiliation

    Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative acyl-CoA dehydrogenase AidB
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
541Escherichia coli K-12Mutation(s): 0 
Gene Names: aidBb4187JW5867
EC: 1.3.99
Find proteins for P33224 (Escherichia coli (strain K12))
Explore P33224 
Go to UniProtKB:  P33224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33224
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
EA [auth J]
GA [auth K]
IA [auth L]
AA [auth H],
CA [auth I],
EA [auth J],
GA [auth K],
IA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
C27 H33 N9 O15 P2
Query on CL

Download Ideal Coordinates CCD File 
BA [auth H]
DA [auth I]
FA [auth J]
HA [auth K]
JA [auth L]
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.72α = 90
b = 179.72β = 90
c = 204.237γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description