4QTO

1.65 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus with BME-modified Cys289 and PEG molecule in active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1107/S1399004715004228
  • Primary Citation of Related Structures:  
    4NU9, 4Q92, 4QJE, 4QN2, 4NEA, 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Betaine aldehyde dehydrogenaseA, B, C, D520Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: betBSACOL2628
EC: 1.2.1.8
Find proteins for A0A0H2X0S3 (Staphylococcus aureus (strain COL))
Explore A0A0H2X0S3 
Go to UniProtKB:  A0A0H2X0S3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
S [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], M [auth B], R [auth C], V [auth D]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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

Download Ideal Coordinates CCD File 
H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], W [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
T [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A], L [auth B], Q [auth C], U [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B, C, DL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.249α = 90
b = 102.474β = 104.45
c = 118.178γ = 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: 2014-07-16
    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