4QN2

2.6 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) in complex with NAD+ and BME-free Cys289


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus.

Halavaty, A.S.Rich, R.L.Chen, C.Joo, J.C.Minasov, G.Dubrovska, I.Winsor, J.R.Myszka, D.G.Duban, M.Shuvalova, L.Yakunin, A.F.Anderson, W.F.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1159-1175

  • DOI: https://doi.org/10.1107/S1399004715004228
  • Primary Citation of Related Structures:  
    4NEA, 4NU9, 4Q92, 4QJE, 4QN2, 4QTO

  • PubMed Abstract: 

    When exposed to high osmolarity, methicillin-resistant Staphylococcus aureus (MRSA) restores its growth and establishes a new steady state by accumulating the osmoprotectant metabolite betaine. Effective osmoregulation has also been implicated in the acquirement of a profound antibiotic resistance by MRSA. Betaine can be obtained from the bacterial habitat or produced intracellularly from choline via the toxic betaine aldehyde (BA) employing the choline dehydrogenase and betaine aldehyde dehydrogenase (BADH) enzymes. Here, it is shown that the putative betaine aldehyde dehydrogenase SACOL2628 from the early MRSA isolate COL (SaBADH) utilizes betaine aldehyde as the primary substrate and nicotinamide adenine dinucleotide (NAD(+)) as the cofactor. Surface plasmon resonance experiments revealed that the affinity of NAD(+), NADH and BA for SaBADH is affected by temperature, pH and buffer composition. Five crystal structures of the wild type and three structures of the Gly234Ser mutant of SaBADH in the apo and holo forms provide details of the molecular mechanisms of activity and substrate specificity/inhibition of this enzyme.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Betaine aldehyde dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
517Staphylococcus aureus subsp. aureus COLMutation(s): 1 
Gene Names: betBSACOL2628
EC: 1.2.1.8
UniProt
Find proteins for A0A0H2X0S3 (Staphylococcus aureus (strain COL))
Explore A0A0H2X0S3 
Go to UniProtKB:  A0A0H2X0S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2X0S3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
L [auth C]
M [auth D]
N [auth E]
I [auth A],
J [auth B],
L [auth C],
M [auth D],
N [auth E],
O [auth F],
P [auth G],
Q [auth H]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
K [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.592α = 90
b = 168.368β = 104.92
c = 144.523γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description