8KHM

Crystal structure of human methionine aminopeptidase 12 (MAP12) in the unbound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural insights into N-terminal methionine cleavage by the human mitochondrial methionine aminopeptidase, MetAP1D.

Lee, Y.Kim, H.Lee, E.Hahn, H.Heo, Y.Jang, D.M.Kwak, K.Kim, H.J.Kim, H.S.

(2023) Sci Rep 13: 22326-22326

  • DOI: https://doi.org/10.1038/s41598-023-49332-6
  • Primary Citation of Related Structures:  
    8KHM, 8KHN, 8KHO

  • PubMed Abstract: 

    Isozymes are enzymes that catalyze identical biological reactions, yet exhibit slight variations in structures and catalytic efficiency, which enables the precise adjustment of metabolism to fulfill the specific requirements of a particular tissue or stage of development. Methionine aminopeptidase (MetAP) isozymes function a critical role in cleaving N-terminal methionine from nascent proteins to generate functional proteins. In humans, two distinct MetAP types I and II have been identified, with type I further categorized into cytosolic (MetAP1) and mitochondrial (MetAP1D) variants. However, despite extensive structural studies on both bacterial and human cytosolic MetAPs, the structural information remains unavailable for human mitochondrial MetAP. This study was aimed to elucidate the high-resolution structures of human mitochondrial MetAP1D in its apo-, cobalt-, and methionine-bound states. Through a comprehensive analysis of the determined structures and a docking simulation model with mitochondrial substrate peptides, we present mechanistic insights into the cleavage process of the initiator methionine from mitochondrial proteins. Notably, despite the shared features at the active site between the cytosolic and mitochondrial MetAP type I isozymes, we identified distinct structural disparities within the active-site pocket primarily contributed by two specific loops that could play a role in accommodating specific substrates. These structural insights offer a basis for the further exploration of MetAP isozymes as critical players in cellular processes and potential therapeutic applications.


  • Organizational Affiliation

    Research Institute, National Cancer Center, Goyang, 10408, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase 1D, mitochondrial313Homo sapiensMutation(s): 0 
Gene Names: METAP1DMAP1D
EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UB28 (Homo sapiens)
Explore Q6UB28 
Go to UniProtKB:  Q6UB28
PHAROS:  Q6UB28
GTEx:  ENSG00000172878 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UB28
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.398α = 90
b = 81.204β = 102.33
c = 48.893γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-00207997
Other governmentICR-21-05
Other governmentICR-22-05
Other privateNCC-2210390
Other privateNCC-2210730

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release