5ZHZ

Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of the apurinic/apyrimidinic endonuclease IV from Mycobacterium tuberculosis.

Zhang, W.Xu, Y.Yan, M.Li, S.Wang, H.Yang, H.Zhou, W.Rao, Z.

(2018) Biochem Biophys Res Commun 498: 111-118

  • DOI: 10.1016/j.bbrc.2018.02.181
  • Primary Citation of Related Structures:  
    5ZHZ

  • PubMed Abstract: 
  • Endonuclease IV is a typical endonuclease of the apurinic-apyrimidinic (AP) or abasic endonuclease superfamily. It repairs damaged DNA through base excision repair by cleaving the DNA backbone immediately 5' of an AP site. In Mycobacterium tuberculos ...

    Endonuclease IV is a typical endonuclease of the apurinic-apyrimidinic (AP) or abasic endonuclease superfamily. It repairs damaged DNA through base excision repair by cleaving the DNA backbone immediately 5' of an AP site. In Mycobacterium tuberculosis, endonuclease IV is the major AP endonuclease. This enzyme is absent from mammalian cells, making it an attractive target for anti-tuberculosis drug development. In this study, the structure of the recombinant endonuclease IV from M. tuberculosis (MtbEndo IV) was determined at a high resolution of 1.18 Å. MtbEndo IV was found to have a classical α8β8-fold TIM barrel with loops on its surface connecting the α-helices and β-strands that constitute a groove for DNA binding. Three zinc ions were identified at the active site. A comparison between the structures of MtbEndo IV and Escherichia coli End IV suggested that Gln32 of MtbEndo IV may plays a role in regulating substrate binding.


    Organizational Affiliation

    College of Life Sciences, College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable endonuclease 4A258Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: endnfoRv0670MTCI376.04c
EC: 3.1.21.2
Find proteins for P9WQ13 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQ13 
Go to UniProtKB:  P9WQ13
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.638α = 90
b = 55.269β = 90
c = 102.939γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Key R&D Program of ChinaChina2017YFC0840300
MOST 973 ProjectChinaNo. 2014CB542800
MOST 973 ProjectChinaNo. 2014CBA02003
CAS SPR program BChinaXDB08020200
National Science Foundation of ChinaChina81330036 and 81520108019

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release