7W2I

Crystal structure of LOG (Rv1205) from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the cytokinin-producing enzyme "lonely guy" (LOG) from Mycobacterium tuberculosis.

Shang, L.Li, G.Lin, Q.Ou, M.Liang, J.Xiao, G.Wang, Z.Cui, S.Zhang, T.Liu, L.Zhang, G.

(2022) Biochem Biophys Res Commun 598: 113-118

  • DOI: https://doi.org/10.1016/j.bbrc.2022.01.103
  • Primary Citation of Related Structures:  
    7W2I

  • PubMed Abstract: 

    Mycobacterium tuberculosis (Mtb) is an extremely successful intracellular pathogen that cause a large number of death worldwide. It is interesting that this non-phytopathogen can synthesize cytokinin by "lonely guy" (LOG) protein. The cytokinin biosynthesis pathway in Mtb is not clear. Here we determined the crystal structure of LOG from Mtb (MtLOG) at a high resolution of 1.8 Å. MtLOG exists as dimer which belongs to type-I LOG and shows a typical α-β Rossmann fold. Like other LOGs, MtLOG also contains a conserved "PGGXGTXXE" motif that contributes to the formation of an active site. For the first time, we found that the MtLOG binds to Mg 2+ in the negative potential pocket. According to the docking result, we found that Arg78, Arg98 and Tyr162 should be the key amino acid involved in substrate binding. Our findings provide a structural basis for cytokinin study in Mtb and will play an important role in design and development of enzyme inhibitors.


  • Organizational Affiliation

    State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510700, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokinin riboside 5'-monophosphate phosphoribohydrolase183Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 3.2.2
UniProt
Find proteins for O05306 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O05306 
Go to UniProtKB:  O05306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05306
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokinin riboside 5'-monophosphate phosphoribohydrolase
B, C, D
177Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 3.2.2
UniProt
Find proteins for O05306 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O05306 
Go to UniProtKB:  O05306
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05306
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A],
K [auth C],
M [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
J [auth C],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.958α = 90
b = 75.976β = 90
c = 134.953γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government2019B1515120041

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description