3A73

Crystal Structure Analysis of Human serum albumin complexed with delta 12-prostaglandin J2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Delta12-prostaglandin J2 as a product and ligand of human serum albumin: formation of an unusual covalent adduct at His146.

Yamaguchi, S.Aldini, G.Ito, S.Morishita, N.Shibata, T.Vistoli, G.Carini, M.Uchida, K.

(2010) J.Am.Chem.Soc. 132: 824-832

  • DOI: 10.1021/ja908878n

  • PubMed Abstract: 
  • Human serum albumin (HSA), the most abundant protein in plasma, has a very unique function, catalyzing the conversion of prostaglandin J(2) (PGJ(2)), a dehydration product of PGD(2), to yield Delta(12)-PGJ(2). These PGD(2) metabolites are actively tr ...

    Human serum albumin (HSA), the most abundant protein in plasma, has a very unique function, catalyzing the conversion of prostaglandin J(2) (PGJ(2)), a dehydration product of PGD(2), to yield Delta(12)-PGJ(2). These PGD(2) metabolites are actively transported into cells and accumulated in the nuclei, where they act as potent inducers of cell growth inhibition and cell differentiation, and exhibit their own unique spectrum of biological effects. The facts that (i) arachidonic acid metabolites bind to human serum albumin (HSA) and the metabolism of these molecules is altered as a result of binding, (ii) HSA catalyzes the transformation of PGJ(2) into Delta(12)-PGJ(2), and (iii) Delta(12)-PGJ(2) is stable in serum suggest that HSA may bind and stabilize Delta(12)-PGJ(2) in a specific manner. A molecular interaction analysis using surface plasmon resonance (Biacore) indeed suggested the presence of a specific Delta(12)-PGJ(2)-binding site in HSA. To investigate the molecular details of the binding of this PGD(2) metabolite to albumin, we analyzed the cocrystal structure of the HSA-Delta(12)-PGJ(2)-myristate complex by X-ray crystallography and found that two Delta(12)-PGJ(2) molecules bind to a primary site in subdomain IB of the protein. The electron density results suggested that one of the two Delta(12)-PGJ(2) molecules that specifically bind to the site covalently interacted with a histidine residue (His146). Using nano-LC-MS/MS analysis of the HSA-Delta(12)-PGJ(2) complex, the formation of an unusual Delta(12)-PGJ(2)-histidine adduct at His146 was confirmed. Thus, our crystallographic and mass spectrometric analyses of the HSA-Delta(12)-PGJ(2) complex provided intriguing new insights into the molecular details of how this electrophilic ligand interacts with its primary producer and transporter.


    Organizational Affiliation

    Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serum albumin
A, B
585Homo sapiensMutation(s): 0 
Gene Names: ALB
Find proteins for P02768 (Homo sapiens)
Go to Gene View: ALB
Go to UniProtKB:  P02768
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
A, B
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
PJ2
Query on PJ2

Download SDF File 
Download CCD File 
A, B
(5Z,12Z,15S)-15-hydroxy-11-oxoprosta-5,9,12-trien-1-oic acid
delta12-prostaglandine J2
C20 H30 O4
TUXFWOHFPFBNEJ-WHYHPIPXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PJ2Kd: 420000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.229 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 38.060α = 74.80
b = 92.047β = 89.53
c = 94.664γ = 80.21
Software Package:
Software NamePurpose
MLPHAREphasing
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-09-11 
  • Released Date: 2010-01-19 
  • Deposition Author(s): Ito, S.

Revision History 

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2013-10-23
    Type: Database references