7W2I | pdb_00007w2i

Crystal structure of LOG (Rv1205) from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb7W2I/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-23 Released: 2022-07-06
Deposition Author(s): Shang, L., Zhang, G.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.214 (Depositor), 0.223 (DCC)
R-Value Work:
0.165 (Depositor), 0.177 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
View more details

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

PubMed: 35158209 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2022.01.103
Primary Citation 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

National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China.

Macromolecule Content

Total Structure Weight: 77.15 kDa
Atom Count: 6,154
Modeled Residue Count: 714
Deposited Residue Count: 714
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokinin riboside 5'-monophosphate phosphoribohydrolase	A	183	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377... yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377, ERS027646_02317, ERS027661_02284, FPJ30_06615, FPJ31_06635, FPJ32_06600, FPJ33_06635, FPJ34_06605, FPJ35_06645, FPJ36_06610, FPJ37_06625, FPJ38_06685, FPJ39_06605, FPJ40_06630, FPJ41_06610, FPJ42_06600, FPJ43_06625, FPJ44_06630, FPJ45_06605, FPJ46_06605, FPJ47_06620, FPJ48_06590, FPJ49_06625, FPJ50_06605, FPJ51_06600, FPJ52_06615, FPJ53_06605, FPJ54_06615, FPJ55_06630, FPJ56_06605, FPJ57_06600, FPJ58_06625, FPJ59_06615, FPJ60_06630, FPJ61_06605, FPJ62_06605, FPJ63_06620, FPJ64_06630, FPJ65_06615, FPJ66_06605, FPJ67_06650, FPJ69_06650, FPJ70_06650, FPJ71_06650, FPJ72_05390, FPJ73_06605, FPJ76_06570, FPJ77_06635, FPJ78_06620, FPJ79_06645, FPJ80_06625, FPJ81_06635, FPJ82_06640, FPJ83_14970, FPJ84_06625, FPJ85_14960, FPJ86_14950, FPJ87_14955, FPJ88_06580, FPJ89_06625, FPJ90_06600, FPJ91_06645, FPJ92_06600, FPJ93_06635, FPJ94_05385, FPJ95_06625, FPJ96_06640, FPJ97_06645, FPJ98_06615, FPJ99_06640, FPK00_06610, FPK01_06670, FPK02_06615, FPK03_06630, FPK04_06630, FPK05_06625, FPK06_06610, FPK07_06620, FPK08_06630, FPK09_06625, FPK10_05385, FPK11_06625, FPK12_06590, FPK13_06620, FPK14_06625, FPK16_06620, FPK17_06620, FPK18_06620, FPK19_06635, FPK20_06635, FPK21_06605, FPK22_06630, HRD52_06340, HRD53_06340, SAMEA2683035_01466 EC: 3.2.2
UniProt
Find proteins for O05306 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O05306 Go to UniProtKB: O05306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O05306
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokinin riboside 5'-monophosphate phosphoribohydrolase	B, C, D	177	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377... yvdD, E5M05_07430, E5M52_06270, ERS007670_00485, ERS007683_01414, ERS007703_01029, ERS007720_04465, ERS007722_04210, ERS013440_03167, ERS024276_02377, ERS027646_02317, ERS027661_02284, FPJ30_06615, FPJ31_06635, FPJ32_06600, FPJ33_06635, FPJ34_06605, FPJ35_06645, FPJ36_06610, FPJ37_06625, FPJ38_06685, FPJ39_06605, FPJ40_06630, FPJ41_06610, FPJ42_06600, FPJ43_06625, FPJ44_06630, FPJ45_06605, FPJ46_06605, FPJ47_06620, FPJ48_06590, FPJ49_06625, FPJ50_06605, FPJ51_06600, FPJ52_06615, FPJ53_06605, FPJ54_06615, FPJ55_06630, FPJ56_06605, FPJ57_06600, FPJ58_06625, FPJ59_06615, FPJ60_06630, FPJ61_06605, FPJ62_06605, FPJ63_06620, FPJ64_06630, FPJ65_06615, FPJ66_06605, FPJ67_06650, FPJ69_06650, FPJ70_06650, FPJ71_06650, FPJ72_05390, FPJ73_06605, FPJ76_06570, FPJ77_06635, FPJ78_06620, FPJ79_06645, FPJ80_06625, FPJ81_06635, FPJ82_06640, FPJ83_14970, FPJ84_06625, FPJ85_14960, FPJ86_14950, FPJ87_14955, FPJ88_06580, FPJ89_06625, FPJ90_06600, FPJ91_06645, FPJ92_06600, FPJ93_06635, FPJ94_05385, FPJ95_06625, FPJ96_06640, FPJ97_06645, FPJ98_06615, FPJ99_06640, FPK00_06610, FPK01_06670, FPK02_06615, FPK03_06630, FPK04_06630, FPK05_06625, FPK06_06610, FPK07_06620, FPK08_06630, FPK09_06625, FPK10_05385, FPK11_06625, FPK12_06590, FPK13_06620, FPK14_06625, FPK16_06620, FPK17_06620, FPK18_06620, FPK19_06635, FPK20_06635, FPK21_06605, FPK22_06630, HRD52_06340, HRD53_06340, SAMEA2683035_01466 EC: 3.2.2
UniProt
Find proteins for O05306 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O05306 Go to UniProtKB: O05306
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O05306
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth A]	F [auth A], H [auth A], K [auth C], M [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth C] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain E [auth A]	E [auth A], I [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain L [auth D]