7V1Y

Serine beta-lactamase-like protein LACTB in complex with inhibitor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for the catalytic activity of filamentous human serine beta-lactamase-like protein LACTB.

Zhang, M.Zhang, L.Guo, R.Xiao, C.Yin, J.Zhang, S.Yang, M.

(2022) Structure 30: 685-696.e5

  • DOI: https://doi.org/10.1016/j.str.2022.02.007
  • Primary Citation of Related Structures:  
    7V1Y, 7V1Z, 7V21

  • PubMed Abstract: 

    Serine beta-lactamase-like protein (LACTB) is a mammalian mitochondrial serine protease that can specifically hydrolyze peptide bonds adjacent to aspartic acid residues and is structurally related to prokaryotic penicillin-binding proteins. Here, we determined the cryoelectron microscopy structures of human LACTB (hLACTB) filaments from wild-type protein, a middle region deletion mutant, and in complex with the inhibitor Z-AAD-CMK at 3.0-, 3.1-, and 2.8-Å resolution, respectively. Structural analysis and activity assays revealed that three interfaces are required for the assembly of hLACTB filaments and that the formation of higher order helical structures facilitates its cleavage activity. Further structural and enzymatic analyses of middle region deletion constructs indicated that, while this region is necessary for substrate hydrolysis, it is not required for filament formation. Moreover, the inhibitor-bound structure showed that hLACTB may cleave peptide bonds adjacent to aspartic acid residues. These findings provide the structural basis underlying hLACTB catalytic activity.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine beta-lactamase-like protein LACTB, mitochondrialA,
B [auth C],
C [auth B],
D
487Homo sapiensMutation(s): 0 
Gene Names: LACTBMRPL56UNQ843/PRO1781
EC: 3.4
UniProt & NIH Common Fund Data Resources
Find proteins for P83111 (Homo sapiens)
Explore P83111 
Go to UniProtKB:  P83111
PHAROS:  P83111
GTEx:  ENSG00000103642 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83111
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-B3S
E, F, G, H
3synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31671049

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection