Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 132.21 kDa 
• Atom Count: 9,982 
• Modelled Residue Count: 1,104 
• Deposited Residue Count: 1,104 
• Unique protein chains: 1

 5F19

The Crystal Structure of Aspirin Acetylated Human Cyclooxygenase-2

• PDB DOI: 10.2210/pdb5F19/pdb

• Classification: OXIDOREDUCTASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2015-11-30 Released: 2016-03-16 
• Deposition Author(s): Lucido, M.J., Orlando, B.J., Malkowski, M.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.207 
• R-Value Work: 0.168 
• R-Value Observed: 0.172 

Literature

Crystal Structure of Aspirin-Acetylated Human Cyclooxygenase-2: Insight into the Formation of Products with Reversed Stereochemistry.

Lucido, M.J., Orlando, B.J., Vecchio, A.J., Malkowski, M.G.

(2016) Biochemistry 55: 1226-1238

• PubMed: 26859324 
• DOI: 10.1021/acs.biochem.5b01378
• Primary Citation of Related Structures:  
  5F19, 5F1A, 5FDQ


• PubMed Abstract: 
  

Aspirin and other nonsteroidal anti-inflammatory drugs target the cyclooxygenase enzymes (COX-1 and COX-2) to block the formation of prostaglandins. Aspirin is unique in that it covalently modifies each enzyme by acetylating Ser-530 within the cyclooxygenase active site. Acetylation of COX-1 leads to complete loss of activity, while acetylation of COX-2 results in the generation of the monooxygenated product 15(R)-hydroxyeicosatetraenoic acid (15R-HETE). Ser-530 has also been shown to influence the stereochemistry for the addition of oxygen to the prostaglandin product. We determined the crystal structures of S530T murine (mu) COX-2, aspirin-acetylated human (hu) COX-2, and huCOX-2 in complex with salicylate to 1.9, 2.0, and 2.4 Å, respectively. The structures reveal that (1) the acetylated Ser-530 completely blocks access to the hydrophobic groove, (2) the observed binding pose of salicylate is reflective of the enzyme-inhibitor complex prior to acetylation, and (3) the observed Thr-530 rotamer in the S530T muCOX-2 crystal structure does not impede access to the hydrophobic groove. On the basis of these structural observations, along with functional analysis of the S530T/G533V double mutant, we propose a working hypothesis for the generation of 15R-HETE by aspirin-acetylated COX-2. We also observe differential acetylation of COX-2 purified in various detergent systems and nanodiscs, indicating that detergent and lipid binding within the membrane-binding domain of the enzyme alters the rate of the acetylation reaction in vitro.

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Organizational Affiliation: 

Department of Structural Biology, The State University of New York at Buffalo and Hauptman-Woodward Medical Research Institute , Buffalo, New York 14203, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin G/H synthase 2	A, B	552	Homo sapiens	Mutation(s): 0  Gene Names: PTGS2, COX2 EC: 1.14.99.1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P35354 (Homo sapiens) Explore P35354  Go to UniProtKB:  P35354
PHAROS:  P35354

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COH	F [auth A], R [auth B]	PROTOPORPHYRIN IX CONTAINING CO C34 H32 Co N4 O4 AQTFKGDWFRRIHR-CTESUSPADG
BOG	DA [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
NAG	G [auth A], H [auth A], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
AKR	I [auth A], J [auth A], T [auth B], U [auth B]	ACRYLIC ACID C3 H4 O2 NIXOWILDQLNWCW-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], CA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OAS	A, B	L-PEPTIDE LINKING	C5 H9 N O4		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.207 
• R-Value Work: 0.168 
• R-Value Observed: 0.172 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.2	α = 90
b = 130.13	β = 90
c = 178.03	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Lucido, M.J., Orlando, B.J., Malkowski, M.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM077176

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Refinement description
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary