4KJD

RatIntestinal AP expressed in E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of rat intestinal alkaline phosphatase - Role of crown domain in mammalian alkaline phosphatases.

Ghosh, K.Mazumder Tagore, D.Anumula, R.Lakshmaiah, B.Kumar, P.P.Singaram, S.Matan, T.Kallipatti, S.Selvam, S.Krishnamurthy, P.Ramarao, M.

(2013) J.Struct.Biol. 184: 182-192

  • DOI: 10.1016/j.jsb.2013.09.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Intestinal alkaline phosphatases (IAPs) are involved in the cleavage of phosphate prodrugs to liberate the drug for absorption in the intestine. To facilitate in vitro characterization of phosphate prodrugs, we have cloned, expressed, purified and ch ...

    Intestinal alkaline phosphatases (IAPs) are involved in the cleavage of phosphate prodrugs to liberate the drug for absorption in the intestine. To facilitate in vitro characterization of phosphate prodrugs, we have cloned, expressed, purified and characterized IAPs from rat and cynomolgus monkey (rIAP and cIAP respectively) which are important pre-clinical species for drug metabolism studies. The recombinant rat and monkey enzymes expressed in Sf9 insect cells (IAP-Ic) were found to be glycosylated and active. Expression of rat IAP in Escherichia coli (rIAP-Ec) led to ~200-fold loss of activity that was partially recovered by the addition of external Zn(2+) and Mg(2+) ions. Crystal structures of rIAP-Ec and rIAP-Ic were determined and they provide rationale for the discrepancy in enzyme activities. Rat IAP-Ic retains its activity in presence of both Zn(2+) and Mg(2+) whereas activity of most other alkaline phosphatases (APs) including the cIAP was strongly inhibited by excess Zn(2+). Based on our crystal structure, we hypothesized the residue Q317 in rIAP, present within 7 Å of the Mg(2+) at M3, to be important for this difference in activity. The Q317H rIAP and H317Q cIAP mutants showed reversal in effect of Zn(2+), corroborating the hypothesis. Further analysis of the two structures indicated a close linkage between glycosylation and crown domain stability. A triple mutant of rIAP, where all the three putative N-linked glycosylation sites were mutated showed thermal instability and reduced activity.


    Organizational Affiliation

    Applied Biotechnology, Biocon Bristol-Myers Squibb Research and Development Center, Syngene International Ltd., Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore 560099, India. Electronic address: Kaushik.Ghosh@syngeneintl.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Intestinal-type alkaline phosphatase 1
A, B
488Rattus norvegicusMutation(s): 0 
Gene Names: Alpi
EC: 3.1.3.1
Find proteins for P15693 (Rattus norvegicus)
Go to UniProtKB:  P15693
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.321α = 90.00
b = 75.726β = 90.00
c = 170.710γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references