4AD9

Crystal structure of human LACTB2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Identification of Lactb2, a Metallo-Beta-Lactamase Protein, as a Human Mitochondrial Endoribonuclease

Allerston, C.K.Gileadi, O.Levy, S.Liveanu, V.Rohana, M.Schuster, G.

(2016) Nucleic Acids Res 44: 1813

  • DOI: 10.1093/nar/gkw050
  • Primary Citation of Related Structures:  
    4AD9

  • PubMed Abstract: 
  • Post-transcriptional control of mitochondrial gene expression, including the processing and generation of mature transcripts as well as their degradation, is a key regulatory step in gene expression in human mitochondria. Consequently, identification of the proteins responsible for RNA processing and degradation in this organelle is of great importance ...

    Post-transcriptional control of mitochondrial gene expression, including the processing and generation of mature transcripts as well as their degradation, is a key regulatory step in gene expression in human mitochondria. Consequently, identification of the proteins responsible for RNA processing and degradation in this organelle is of great importance. The metallo-β-lactamase (MBL) is a candidate protein family that includes ribo- and deoxyribonucleases. In this study, we discovered a function for LACTB2, an orphan MBL protein found in mammalian mitochondria. Solving its crystal structure revealed almost perfect alignment of the MBL domain with CPSF73, as well as to other ribonucleases of the MBL superfamily. Recombinant human LACTB2 displayed robust endoribonuclease activity on ssRNA with a preference for cleavage after purine-pyrimidine sequences. Mutational analysis identified an extended RNA-binding site. Knockdown of LACTB2 in cultured cells caused a moderate but significant accumulation of many mitochondrial transcripts, and its overexpression led to the opposite effect. Furthermore, manipulation of LACTB2 expression resulted in cellular morphological deformation and cell death. Together, this study discovered that LACTB2 is an endoribonuclease that is involved in the turnover of mitochondrial RNA, and is essential for mitochondrial function in human cells.


    Organizational Affiliation

    Faculty of Biology, Technion- Israel Institute of Technology, Haifa 32000, Israel gadis@tx.technion.ac.il.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-LACTAMASE-LIKE PROTEIN 2A, B, C, D, E, F289Homo sapiensMutation(s): 0 
Gene Names: LACTB2CGI-83
EC: 3 (PDB Primary Data), 3.1.27 (UniProt)
Find proteins for Q53H82 (Homo sapiens)
Explore Q53H82 
Go to UniProtKB:  Q53H82
NIH Common Fund Data Resources
PHAROS:  Q53H82
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , J [auth B] , K [auth B] , L [auth C] , M [auth C] , N [auth D] , O [auth D] , 
G [auth A],  H [auth A],  J [auth B],  K [auth B],  L [auth C],  M [auth C],  N [auth D],  O [auth D],  R [auth E],  S [auth E],  T [auth F],  U [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A], P [auth D], Q [auth D], V [auth F]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.47α = 90
b = 95.69β = 112.84
c = 135.76γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Atomic model, Database references, Other
  • Version 1.2: 2016-03-16
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Structure summary