6U7A

Rv3722c in complex with kynurenine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase
A, B, C, D, E
A, B, C, D, E, F, G, H
435Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for O69689 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O69689 
Go to UniProtKB:  O69689
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69689
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q0P (Subject of Investigation/LOI)
Query on Q0P

Download Ideal Coordinates CCD File 
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
PMP
Query on PMP

Download Ideal Coordinates CCD File 
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
PLP
Query on PLP

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BA [auth E],
EA [auth F],
NA [auth H]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
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
KYA (Subject of Investigation/LOI)
Query on KYA

Download Ideal Coordinates CCD File 
FA [auth G],
N [auth B],
S [auth C],
W [auth D]
4-hydroxyquinoline-2-carboxylic acid
C10 H7 N O3
HCZHHEIFKROPDY-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.398α = 90
b = 108.398β = 90
c = 321.344γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description