7KAZ | pdb_00007kaz

Crystal structure of OhyA(E82A)-18:1/h18:0-FAD complex from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb7KAZ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-10-01 Released: 2021-01-06 
• Deposition Author(s): Radka, C.D., Rock, C.O.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structure and mechanism of Staphylococcus aureus oleate hydratase (OhyA).

Radka, C.D., Batte, J.L., Frank, M.W., Young, B.M., Rock, C.O.

(2021) J Biological Chem 296: 100252-100252

• PubMed: 33376139 
• DOI: https://doi.org/10.1074/jbc.RA120.016818
• Primary Citation Related Structures: 
  7KAV, 7KAW, 7KAX, 7KAY, 7KAZ


• PubMed Abstract: 
  

  Flavin adenine dinucleotide (FAD)-dependent bacterial oleate hydratases (OhyAs) catalyze the addition of water to isolated fatty acid carbon-carbon double bonds. Staphylococcus aureus uses OhyA to counteract the host innate immune response by inactivating antimicrobial unsaturated fatty acids. Mechanistic information explaining how OhyAs catalyze regiospecific and stereospecific hydration is required to understand their biological functions and the potential for engineering new products. In this study, we deduced the catalytic mechanism of OhyA from multiple structures of S. aureus OhyA in binary and ternary complexes with combinations of ligands along with biochemical analyses of relevant mutants. The substrate-free state shows Arg81 is the gatekeeper that controls fatty acid entrance to the active site. FAD binding engages the catalytic loop to simultaneously rotate Glu82 into its active conformation and Arg81 out of the hydrophobic substrate tunnel, allowing the fatty acid to rotate into the active site. FAD binding also dehydrates the active site, leaving a single water molecule connected to Glu82. This active site water is a hydronium ion based on the analysis of its hydrogen bond network in the OhyA•PEG400•FAD complex. We conclude that OhyA accelerates acid-catalyzed alkene hydration by positioning the fatty acid double bond to attack the active site hydronium ion, followed by the addition of water to the transient carbocation intermediate. Structural transitions within S. aureus OhyA channel oleate to the active site, curl oleate around the substrate water, and stabilize the hydroxylated product to inactivate antimicrobial fatty acids.

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Organizational Affiliation: 
• The Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
The Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 211.98 kDa 
• Atom Count: 16,992 
• Modeled Residue Count: 1,746 
• Deposited Residue Count: 1,833 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oleate hydratase	A [auth C], B, C [auth A]	611	Staphylococcus aureus	Mutation(s): 1  Gene Names:  DD547_00094, DQV53_00770, EP54_06595, EQ90_12415, G0V24_00735, G0X12_00605, G0Z18_00840, G6Y10_10285, GO746_00220, GO803_11440, GO805_08895, GO821_10135, GO894_07145, GO942_14045, HMPREF3211_02399, NCTC10654_00136, RK64_00980 EC: 4.2.1.53
UniProt
Find proteins for A0A0D6GJV1 (Staphylococcus aureus) Explore A0A0D6GJV1  Go to UniProtKB:  A0A0D6GJV1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	E [auth C], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
WAD (Subject of Investigation/LOI)	D [auth C]	(10R)-10-hydroxyoctadecanoic acid C18 H36 O3 PAZZVPKITDJCPV-QGZVFWFLSA-N
OLA (Subject of Investigation/LOI)	G [auth B], I [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
K	F [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.022	α = 90
b = 113.085	β = 116.91
c = 118.393	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
KYLIN	data reduction
KYLIN	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-01-06 
Deposition Author(s): Radka, C.D., Rock, C.O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM034496
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA21765

Revision History  

• Version 1.0: 2021-01-06
  Type: Initial release
  
• Version 1.1: 2021-01-13
  Changes: Database references
• Version 1.2: 2021-04-28
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Database references, Refinement description