Crystal structure of argininosuccinate lyase from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 2.78 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
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Crystal structure and biochemical study on argininosuccinate lyase from Mycobacterium tuberculosis.

Chen, X.B.Chen, J.Zhang, W.Wang, H.Liu, X.Zhou, W.Yang, H.Rao, Z.

(2019) Biochem Biophys Res Commun 510: 116-121

  • DOI: https://doi.org/10.1016/j.bbrc.2019.01.061
  • Primary Citation of Related Structures:  
    6IG5, 6IGA

  • PubMed Abstract: 

    Argininosuccinate lyase (ASL) participates in arginine synthesis through catalysing a reversible reaction in which argininosuccinate (AS) converts into arginine and fumarate. ASL from Mycobacterium tuberculosis is essential for its growth. In this work, the crystal structure of the apo form of MtbASL was determined and reveals a tetrameric structure that is essential for its activity since the active sites are formed by residues from three different monomers. Subsequently, we determined the crystal structure of MtbASL-sulfate complex, and the ligand mimics the negatively charged intermediate. The complex structure and mutagenesis studies indicate that residues S282 and H161 might act as a catalytic dyad. A major conformational change in the MtbASL-SO 4 complex structure could be observed upon sulfate binding, and this movement facilitates the interaction between substrate and the residues involved in catalysis. A different conformational change in the C-terminal domain could be observed in the MtbASL-SO 4 complex compared with that in other homologues. This difference may be responsible for the lower activity of MtbASL, which is related to the slow growth rate of M. tuberculosis. The C-terminal domain is a potential allosteric site upon inhibitor binding. The various conformational changes and the diversity of the sequence of the potential allosteric site across the homologues might provide clues for designing selective inhibitors against M. tuberculosis.

  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, China; College of Life Sciences, Nankai University, Tianjin, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Argininosuccinate lyase
A, B, C, D
470Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: argHRv1659MTCY06H11.24
Find proteins for P9WPY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPY7 
Go to UniProtKB:  P9WPY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPY7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.78 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.155α = 90
b = 129.155β = 90
c = 200.137γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina813300237
National Natural Science Foundation of ChinaChina81520108019

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description