6U7A | pdb_00006u7a

Rv3722c in complex with kynurenine

PDB DOI: https://doi.org/10.2210/pdb6U7A/pdb

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

Deposited: 2019-09-01 Released: 2020-05-06
Deposition Author(s): Mandyoli, L., Sacchettini, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.219 (Depositor), 0.219 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-020-15876-8
Primary Citation 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: 384.7 kDa
Atom Count: 27,421
Modeled Residue Count: 3,382
Deposited Residue Count: 3,480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase	A, B, C, D, E A, B, C, D, E, F, G, H	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: 2.6.1.1
UniProt
Find proteins for O69689 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O69689 Go to UniProtKB: O69689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O69689
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q0P (Subject of Investigation/LOI) Query on Q0P Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(2S)-4-(2-aminophenyl)-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-oxobutanoic acid C₁₈ H₂₀ N₃ O₈ P PUWQXAONJQUTHM-SJTXTDJHSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PMP Query on PMP Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain GA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain GA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D] mmCIF format, chain GA [auth G]	GA [auth G], O [auth B], T [auth C], X [auth D]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain GA [auth G] Focus chain O [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain GA [auth G] Focus chain O [auth B] Focus chain T [auth C] Focus chain X [auth D]
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain NA [auth H] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain NA [auth H] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain NA [auth H]	BA [auth E], EA [auth F], NA [auth H]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain NA [auth H] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain NA [auth H]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain CA [auth E] SDF format, chain PA [auth H] SDF format, chain R [auth B] SDF format, chain M [auth A] SDF format, chain DA [auth E] MOL2 format, chain AA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain PA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] MOL2 format, chain DA [auth E] mmCIF format, chain AA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain PA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A] mmCIF format, chain DA [auth E]	AA [auth D] CA [auth E] DA [auth E] M [auth A] PA [auth H] AA [auth D], CA [auth E], DA [auth E], M [auth A], PA [auth H], R [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain M [auth A] Focus chain PA [auth H] Focus chain R [auth B] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain M [auth A] Focus chain PA [auth H] Focus chain R [auth B]
KYA (Subject of Investigation/LOI) Query on KYA Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain N [auth B] MOL2 format, chain FA [auth G] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] mmCIF format, chain FA [auth G] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B]	FA [auth G], N [auth B], S [auth C], W [auth D]	4-hydroxyquinoline-2-carboxylic acid C₁₀ H₇ N O₃ HCZHHEIFKROPDY-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain FA [auth G] Focus chain N [auth B] Focus chain S [auth C] Focus chain W [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain HA [auth G] SDF format, chain Y [auth D] SDF format, chain U [auth C] SDF format, chain OA [auth H] SDF format, chain J [auth A] SDF format, chain IA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] MOL2 format, chain OA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C] mmCIF format, chain OA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth G]	HA [auth G] IA [auth G] J [auth A] OA [auth H] U [auth C] HA [auth G], IA [auth G], J [auth A], OA [auth H], U [auth C], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth A] Focus chain OA [auth H] Focus chain U [auth C] Focus chain Y [auth D] Interactions & Density Focus chain HA [auth G] Focus chain IA [auth G] Focus chain J [auth A] Focus chain OA [auth H] Focus chain U [auth C] Focus chain Y [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain MA [auth G] SDF format, chain LA [auth G] SDF format, chain KA [auth G] SDF format, chain K [auth A] SDF format, chain JA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain MA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain MA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth G]	JA [auth G] K [auth A] KA [auth G] L [auth A] LA [auth G] JA [auth G], K [auth A], KA [auth G], L [auth A], LA [auth G], MA [auth G], P [auth B], Q [auth B], V [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain JA [auth G] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain JA [auth G] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Z [auth D]