5YR6

Human methionine aminopeptidase type 1b (F309L mutant) in complex with TNP470


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history


Literature

Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis.

Pillalamarri, V.Arya, T.Haque, N.Bala, S.C.Marapaka, A.K.Addlagatta, A.

(2019) Biochem J 476: 991-1003

  • DOI: https://doi.org/10.1042/BCJ20180874
  • Primary Citation of Related Structures:  
    5YKP, 5YR4, 5YR5, 5YR6

  • PubMed Abstract: 

    Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs ( Streptococcus pneumoniae and Enterococcus faecalis ) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP ( Hs MetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP ( Hs MetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.


  • Organizational Affiliation

    Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 1304Homo sapiensMutation(s): 1 
Gene Names: METAP1
EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P53582 (Homo sapiens)
Explore P53582 
Go to UniProtKB:  P53582
PHAROS:  P53582
GTEx:  ENSG00000164024 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53582
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TN4
Query on TN4

Download Ideal Coordinates CCD File 
E [auth A](1R,2S,3S,4R)-4-hydroxy-2-methoxy-4-methyl-3-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]cyclohexyl (chloroacetyl)carbamate
C19 H30 Cl N O6
OUUSPVSSNHLIGE-AGYLCKTBSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.439α = 90
b = 77.325β = 91.7
c = 47.759γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIndiaEMR/2015/000461

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 2.0: 2019-02-13
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 2.2: 2019-04-03
    Changes: Data collection, Database references
  • Version 2.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description