5MJ6

Ligand-induced conformational change of Insulin-regulated aminopeptidase: insights on catalytic mechanism and active site plasticity.

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens

  • Deposited: 2016-11-30 Released: 2017-04-05 
  • Deposition Author(s): Mpakali, A., Stratikos, E., Saridakis, E., Giastas, P.
  • Funding Organization(s): European Community's Seventh Framework Programme (FP7/2007-2013); Education and Lifelong Learning? of the National Strategic Reference Framework: Research Funding Program of the General Secretariat for Research & Technology; Harry J. Lloyd Charitable trust 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ligand-Induced Conformational Change of Insulin-Regulated Aminopeptidase: Insights on Catalytic Mechanism and Active Site Plasticity.

Mpakali, A.Saridakis, E.Harlos, K.Zhao, Y.Kokkala, P.Georgiadis, D.Giastas, P.Papakyriakou, A.Stratikos, E.

(2017) J. Med. Chem. 60: 2963-2972

  • DOI: 10.1021/acs.jmedchem.6b01890

  • PubMed Abstract: 
  • Insulin-regulated aminopeptidase (IRAP) is an enzyme with several important biological functions that is known to process a large variety of different peptidic substrates, although the mechanism behind this wide specificity is not clearly understood. ...

    Insulin-regulated aminopeptidase (IRAP) is an enzyme with several important biological functions that is known to process a large variety of different peptidic substrates, although the mechanism behind this wide specificity is not clearly understood. We describe a crystal structure of IRAP in complex with a recently developed bioactive and selective inhibitor at 2.53 Å resolution. In the presence of this inhibitor, the enzyme adopts a novel conformation in which domains II and IV are juxtaposed, forming a hollow structure that excludes external solvent access to the catalytic center. A loop adjacent to the enzyme's GAMEN motif undergoes structural reconfiguration, allowing the accommodation of bulky inhibitor side chains. Atomic interactions between the inhibitor and IRAP that are unique to this conformation can explain the strong selectivity compared to homologous aminopeptidases ERAP1 and ERAP2. This conformation provides insight on IRAP's catalytic cycle and reveals significant active-site plasticity that may underlie its substrate permissiveness.


    Organizational Affiliation

    National Center for Scientific Research Demokritos, Agia Paraskevi , Athens 15310, Greece.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucyl-cystinyl aminopeptidase
A, B
881Homo sapiensMutation(s): 0 
Gene Names: LNPEP (OTASE)
EC: 3.4.11.3
Find proteins for Q9UIQ6 (Homo sapiens)
Go to Gene View: LNPEP
Go to UniProtKB:  Q9UIQ6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BR
Query on BR

Download SDF File 
Download CCD File 
A, B
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
7O2
Query on 7O2

Download SDF File 
Download CCD File 
A, B
[(2~{S})-2-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]carbamoyl]-4,4-diphenyl-butyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid
C35 H40 N3 O4 P
FDAGDZVCWKCEEX-NGYIUDBNSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 112.240α = 90.00
b = 143.170β = 90.00
c = 148.990γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
xia2data scaling
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Community's Seventh Framework Programme (FP7/2007-2013)United KingdomBioStruct-X (grant agreement No 283570)
Education and Lifelong Learning? of the National Strategic Reference Framework: Research Funding Program of the General Secretariat for Research & TechnologyGreecegrant no. ERC-14 to ES
Harry J. Lloyd Charitable trustUnited States--

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references