4AD9 | pdb_00004ad9

Crystal structure of human LACTB2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.224 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4AD9

This is version 1.4 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: https://doi.org/10.1093/nar/gkw050
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 198.67 kDa 
  • Atom Count: 14,225 
  • Modeled Residue Count: 1,715 
  • Deposited Residue Count: 1,734 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-LACTAMASE-LIKE PROTEIN 2
A, B, C, D, E
A, B, C, D, E, F
289Homo sapiensMutation(s): 0 
EC: 3 (PDB Primary Data), 3.1.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q53H82 (Homo sapiens)
Explore Q53H82 
Go to UniProtKB:  Q53H82
PHAROS:  Q53H82
GTEx:  ENSG00000147592 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53H82
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / 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]
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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.224 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
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
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other