3PGT

CRYSTAL STRUCTURE OF HGSTP1-1[I104] COMPLEXED WITH THE GSH CONJUGATE OF (+)-ANTI-BPDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure and function of residue 104 and water molecules in the xenobiotic substrate-binding site in human glutathione S-transferase P1-1.

Ji, X.Blaszczyk, J.Xiao, B.O'Donnell, R.Hu, X.Herzog, C.Singh, S.V.Zimniak, P.

(1999) Biochemistry 38: 10231-10238

  • DOI: 10.1021/bi990668u
  • Primary Citation of Related Structures:  
  • Also Cited By: 6AP9, 5JCW

  • PubMed Abstract: 
  • Two variants of human class pi glutathione (GSH) S-transferase 1-1 with either isoleucine or valine in position 104 (hGSTP1-1[I104] and hGSTP1-1[V104]) have distinct activity toward (+)-anti-7, 8-dihydroxy-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene [ ...

    Two variants of human class pi glutathione (GSH) S-transferase 1-1 with either isoleucine or valine in position 104 (hGSTP1-1[I104] and hGSTP1-1[V104]) have distinct activity toward (+)-anti-7, 8-dihydroxy-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(+)-anti-BPDE]. To elucidate their structure-function relationship, we determined the crystal structures of the two variants in complex with GSBpd, the GSH conjugate of (+)-anti-BPDE, at 2.1 and 2.0 A resolution, respectively. The crystal structures reveal that residue 104 in the xenobiotic substrate-binding site (H-site) dictates the binding modes of the product molecule GSBpd with the following three consequences. First, the distance between the hydroxyl group of Y7 and the sulfur atom of GSBpd is 5.9 A in the hGSTP1-1[I104].GSBpd complex versus 3.2 A in the V104 variant. Second, one of the hydroxyl groups of GSBpd forms a direct hydrogen bond with R13 in hGSTP1-1[V104].GSBpd; in contrast, this hydrogen bond is not observed in the I104 complex. Third, in the hydrophilic portion of the H-site of the I104 complex, five H-site water molecules [Ji, X., et al. (1997) Biochemistry 36, 9690-9702] are observed, whereas in the V104 complex, two of the five have been displaced by the Bpd moiety of GSBpd. Although there is no direct hydrogen bond between Y108 (OH) and the hydroxyl groups of GSBpd, indirect hydrogen bonds mediated by water molecules are observed in both complexes, supporting the previously suggested role of the hydroxyl group of Y108 as an electrophilic participant in the addition of GSH to epoxides.


    Related Citations: 
    • Naturally occurring human glutathione S-transferase GSTP1-1 isoforms with isoleucine and valine in position 104 differ in enzymic properties.
      Zimniak, P.,Nanduri, B.,Pikula, S.,Bandorowicz-Pikula, J.,Singhal, S.S.,Srivastava, S.K.,Awasthi, S.,Awasthi, Y.C.
      (1994) Eur.J.Biochem. 224: 893
    • Three-dimensional structure of class pi glutathione S-transferase from human placenta in complex with S-hexylglutathione at 2.8 A resolution.
      Reinemer, P.,Dirr, H.W.,Ladenstein, R.,Huber, R.,Lo Bello, M.,Federici, G.,Parker, M.W.
      (1992) J.Mol.Biol. 227: 214
    • Structure and function of the xenobiotic substrate-binding site and location of a potential non-substrate-binding site in a class pi glutathione S-transferase.
      Ji, X.,Tordova, M.,O'Donnell, R.,Parsons, J.F.,Hayden, J.B.,Gilliland, G.L.,Zimniak, P.
      (1997) Biochemistry 36: 9690


    Organizational Affiliation

    ABL-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702, USA. jix@ncifcrf.gov




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (GLUTATHIONE S-TRANSFERASE)
A, B
210Homo sapiensMutation(s): 0 
Gene Names: GSTP1 (FAEES3, GST3)
EC: 2.5.1.18
Find proteins for P09211 (Homo sapiens)
Go to Gene View: GSTP1
Go to UniProtKB:  P09211
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GBX
Query on GBX

Download SDF File 
Download CCD File 
A, B
2-AMINO-4-[1-(CARBOXYMETHYL-CARBAMOYL)-2-(9-HYDROXY-7,8-DIOXO-7,8,9,10-TETRAHYDRO-BENZO[DEF]CHRYSEN-10-YLSULFANYL)-ETHYLCARBAMOYL]-BUTYRIC ACID
GLUTATHIONE CONJUGATE OF (+)-ANTI-BPDE
C30 H27 N3 O9 S
DUWOHLGCRJLRRU-HVYZTVOGSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.830α = 90.00
b = 89.710β = 97.76
c = 68.410γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing
SHELXL-97refinement
SHELXLrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-03-22 
  • Released Date: 1999-09-01 
  • Deposition Author(s): Ji, X., Xiao, B.

Revision History 

  • Version 1.0: 1999-09-01
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection
  • Version 1.4: 2019-11-13
    Type: Database references