6FKV

Structure and function of aldehyde dehydrogenase from Thermus thermophilus: An enzyme with an evolutionarily-distinct C-terminal arm (Recombinant protein with shortened C-terminal, ADH508)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension.

Hayes, K.Noor, M.Djeghader, A.Armshaw, P.Pembroke, T.Tofail, S.Soulimane, T.

(2018) Sci Rep 8: 13327-13327

  • DOI: https://doi.org/10.1038/s41598-018-31724-8
  • Primary Citation of Related Structures:  
    6FJX, 6FK3, 6FKU, 6FKV

  • PubMed Abstract: 

    Aldehyde dehydrogenases (ALDH) form a superfamily of dimeric or tetrameric enzymes that catalyze the oxidation of a broad range of aldehydes into their corresponding carboxylic acids with the concomitant reduction of the cofactor NAD(P) into NAD(P)H. Despite their varied polypeptide chain length and oligomerisation states, ALDHs possess a conserved architecture of three domains: the catalytic domain, NAD(P) + binding domain, and the oligomerization domain. Here, we describe the structure and function of the ALDH from Thermus thermophilus (ALDH Tt ) which exhibits non-canonical features of both dimeric and tetrameric ALDH and a previously uncharacterized C-terminal arm extension forming novel interactions with the N-terminus in the quaternary structure. This unusual tail also interacts closely with the substrate entry tunnel in each monomer providing further mechanistic detail for the recent discovery of tail-mediated activity regulation in ALDH. However, due to the novel distal extension of the tail of ALDH Tt and stabilizing termini-interactions, the current model of tail-mediated substrate access is not apparent in ALDH Tt . The discovery of such a long tail in a deeply and early branching phylum such as Deinococcus-Thermus indicates that ALDH Tt may be an ancestral or primordial metabolic model of study. This structure provides invaluable evidence of how metabolic regulation has evolved and provides a link to early enzyme regulatory adaptations.


  • Organizational Affiliation

    Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde dehydrogenase
A, B
517Thermus thermophilus HB27Mutation(s): 0 
Gene Names: TT_C0513
EC: 1.2.1.3
UniProt
Find proteins for Q72KD3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72KD3 
Go to UniProtKB:  Q72KD3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72KD3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
P [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
M [auth B],
N [auth B],
O [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
Q [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
Q [auth B],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.19α = 90
b = 105.19β = 90
c = 314.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description