6U78

Rv3722c in complex with glutamic acid

PDB DOI: https://doi.org/10.2210/pdb6U78/pdb

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

Deposited: 2019-08-31 Released: 2020-05-06
Deposition Author(s): Mandyoli, L., Sacchettini, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.215
R-Value Work: 0.193
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Currently 6U78 does not have a validation slider image.

This is version 1.1 of the entry. See complete history.

Literature

Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis.

Jansen, R.S., Mandyoli, L., Hughes, R., Wakabayashi, S., Pinkham, J.T., Selbach, B., Guinn, K.M., Rubin, E.J., Sacchettini, J.C., Rhee, K.Y.

(2020) Nat Commun 11: 1960-1960

PubMed: 32327655 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-15876-8
Primary Citation of Related Structures:
6U78, 6U7A

PubMed Abstract:
Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis, and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Rv3722c deficiency leads to virulence attenuation in macrophages and mice. Our results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in M. tuberculosis.

Organizational Affiliation

Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.

Macromolecule Content

Total Structure Weight: 190.85 kDa
Atom Count: 13,093
Modelled Residue Count: 1,676
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase	A, B, C, D	435	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: DKC2_3956, DSI35_31455, ERS007661_01687, ERS007663_01945, ERS007665_01586, ERS007670_01863, ERS007672_01473, ERS007679_00092, ERS007681_00098, ERS007688_00789... DKC2_3956, DSI35_31455, ERS007661_01687, ERS007663_01945, ERS007665_01586, ERS007670_01863, ERS007672_01473, ERS007679_00092, ERS007681_00098, ERS007688_00789, ERS007703_00081, ERS007720_02793, ERS007722_01790, ERS023446_00155, ERS024276_02601, ERS027646_02441, ERS027652_01615, ERS027653_01450, ERS027656_00154, ERS027666_02093, ERS031537_01226, ERS124361_00578, EUB07_12880, EUB11_07270, EUB16_18395, SAMEA2682835_06491, SAMEA2682864_02982, SAMEA2683035_02356 EC: 2
UniProt
Find proteins for O69689 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O69689 Go to UniProtKB: O69689
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O69689
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	E [auth A], F [auth B], J [auth C], L [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain J [auth C] Focus chain L [auth D]
GLU (Subject of Investigation/LOI) Query on GLU Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D]	H [auth B], K [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain H [auth B] Focus chain K [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]