6IEN

Substrate/product bound Argininosuccinate lyase from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural studies on M. tuberculosis argininosuccinate lyase and its liganded complex: Insights into catalytic mechanism.

Paul, A.Mishra, A.Surolia, A.Vijayan, M.

(2019) IUBMB Life 71: 643-652

  • DOI: 10.1002/iub.2000
  • Primary Citation of Related Structures:  
    6IEM, 6IEN

  • PubMed Abstract: 
  • Argininosuccinate lyase catalyses the reversible breakdown of argininosuccinate into arginine and fumarate and is known to form tetramers in its quaternary association. The absence of structures involving competent enzymes bound to substrate/products came in the way of the precise elucidation of the catalytic mechanism of this family of proteins ...

    Argininosuccinate lyase catalyses the reversible breakdown of argininosuccinate into arginine and fumarate and is known to form tetramers in its quaternary association. The absence of structures involving competent enzymes bound to substrate/products came in the way of the precise elucidation of the catalytic mechanism of this family of proteins. Crystal structures of the enzyme from Mycobacterium tuberculosis in an unliganded form and its complex with the substrate/products have now been determined at 2.2 and 2.7 Å, respectively. The refinement of the structure of the complex was bedevilled by the presence of a lattice translocation defect. The two tetramers in the apo-crystals and the one in the crystals of the liganded protein, have the same structure except for the movements associated with enzyme action. Each molecule consists of an N-domain, an M-domain, and a C-domain. The molecule consists of four binding sites, each made up of peptide stretches from three subunits. Three binding sites appear to be occupied by the ligand in the transition state, while the products occupy the fourth site. The structure exhibits the movement of a loop in the M-domain and parts of the C-domain. This is the first instance when the appropriate movements are observed in a complex with bound substrate/product. The detailed picture of the binding site, active site residues and the movements associated with catalysis thus obtained, enabled a revisit of the mechanism of action of the enzyme. © 2019 IUBMB Life, 71(5):643-652, 2019.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Argininosuccinate lyaseA, B, C, D470Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: argHRv1659MTCY06H11.24
EC: 4.3.2.1
Find proteins for P9WPY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPY7 
Go to UniProtKB:  P9WPY7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AS1
Query on AS1

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], O [auth D]ARGININOSUCCINATE
C10 H18 N4 O6
KDZOASGQNOPSCU-NTSWFWBYSA-N
 Ligand Interaction
ARG
Query on ARG

Download Ideal Coordinates CCD File 
M [auth C]ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
FUM
Query on FUM

Download Ideal Coordinates CCD File 
F [auth A]FUMARIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-OWOJBTEDSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], K [auth B], L [auth B], N [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.18α = 90
b = 131.35β = 90
c = 145.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references