4QJE

1.85 Angstrom resolution crystal structure of apo betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) with BME-free sulfinic acid form of Cys289

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 1.5 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, C, D
517Staphylococcus aureus subsp. aureus COLMutation(s): 1 
Gene Names: betB, SACOL2628
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
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Betaine aldehyde dehydrogenase517Staphylococcus aureus subsp. aureus COLMutation(s): 1 
Gene Names: betB, SACOL2628
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P
Download Ideal Coordinates CCD File 
T [auth C]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
TRS
Query on TRS
Download Ideal Coordinates CCD File 
I [auth A],
R [auth C],
S [auth C]		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG
Query on PEG
Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
L [auth B]
O [auth C]
P [auth C]
G [auth A],
H [auth A],
L [auth B],
O [auth C],
P [auth C],
Q [auth C],
W [auth D],
X [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
M [auth C]
E [auth A],
F [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
U [auth D],
V [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A, C, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.665α = 90
b = 102.929β = 101.42
c = 118.074γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2015-05-13
    Changes: Database references
  • Version 1.3: 2015-06-03
    Changes: Database references
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description