6OFC | pdb_00006ofc

Crystal structure of M. tuberculosis glutamine-dependent NAD+ synthetase complexed with Sulfonamide derivative 1, pyrophosphate, and glutamine

PDB DOI: https://doi.org/10.2210/pdb6OFC/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis CDC1551
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-03-28 Released: 2020-01-08
Deposition Author(s): Chuenchor, W., Doukov, T.I., Gerratana, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.14 Å
R-Value Free:
0.235 (Depositor), 0.217 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Different ways to transport ammonia in human and Mycobacterium tuberculosis NAD+synthetases.

Chuenchor, W., Doukov, T.I., Chang, K.T., Resto, M., Yun, C.S., Gerratana, B.

(2020) Nat Commun 11: 16-16

PubMed: 31911602 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-019-13845-4
Primary Citation Related Structures:
6OFB, 6OFC

PubMed Abstract:
NAD ⁺ synthetase is an essential enzyme of de novo and recycling pathways of NAD ⁺ biosynthesis in Mycobacterium tuberculosis but not in humans. This bifunctional enzyme couples the NAD ⁺ synthetase and glutaminase activities through an ammonia tunnel but free ammonia is also a substrate. Here we show that the Homo sapiens NAD ⁺ synthetase (hsNadE) lacks substrate specificity for glutamine over ammonia and displays a modest activation of the glutaminase domain compared to tbNadE. We report the crystal structures of hsNadE and NAD ⁺ synthetase from M. tuberculosis (tbNadE) with synthetase intermediate analogues. Based on the observed exclusive arrangements of the domains and of the intra- or inter-subunit tunnels we propose a model for the inter-domain communication mechanism for the regulation of glutamine-dependent activity and NH ₃ transport. The structural and mechanistic comparison herein reported between hsNadE and tbNadE provides also a starting point for future efforts in the development of anti-TB drugs.

Organizational Affiliation

Departments of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.

Macromolecule Content

Total Structure Weight: 303.5 kDa
Atom Count: 20,893
Modeled Residue Count: 2,655
Deposited Residue Count: 2,716
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamine-dependent NAD(+) synthetase	A, B, C, D	679	Mycobacterium tuberculosis CDC1551	Mutation(s): 1 Gene Names: nadE, MT2513 EC: 6.3.5.1
UniProt
Find proteins for P9WJJ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJJ3 Go to UniProtKB: P9WJJ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WJJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SFH (Subject of Investigation/LOI) Query on SFH Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D]	E [auth A] F [auth A] G [auth A] J [auth B] K [auth B] E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], Q [auth C], S [auth D]	5'-O-[(pyridine-3-carbonyl)sulfamoyl]adenosine C₁₆ H₁₇ N₇ O₇ S LBBNJCOHYSTAJW-UBEDBUPSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain S [auth D]
POP (Subject of Investigation/LOI) Query on POP Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
GLN (Subject of Investigation/LOI) Query on GLN Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D]	O [auth B], R [auth C], U [auth D]	GLUTAMINE C₅ H₁₀ N₂ O₃ ZDXPYRJPNDTMRX-VKHMYHEASA-N		Interactions Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain V [auth D] MOL2 format, chain P [auth B] MOL2 format, chain V [auth D] mmCIF format, chain P [auth B] mmCIF format, chain V [auth D]	P [auth B], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain V [auth D] Interactions & Density Focus chain P [auth B] Focus chain V [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth D]	H [auth A], I [auth A], M [auth B], T [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain T [auth D]