8G8K | pdb_00008g8k

Crystal structure of Rv1916 (residues 233-398)

• PDB DOI: https://doi.org/10.2210/pdb8G8K/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-02-18 Released: 2023-06-07 
• Deposition Author(s): Kwai, B.X.C., Bashiri, G., Leung, I.K.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Mycobacterium tuberculosis Rv1916 is an Acetyl-CoA-Binding Protein.

Huang, E.Y., Kwai, B.X.C., Bhusal, R.P., Bashiri, G., Leung, I.K.H.

(2023) Chembiochem 24: e202300162-e202300162

• PubMed: 37211532 
• DOI: https://doi.org/10.1002/cbic.202300162
• Primary Citation of Related Structures:  
  8G8K


• PubMed Abstract: 
  

  Isocitrate lyase (ICL) isoform 2 is an essential enzyme for some clinical Mycobacterium tuberculosis (Mtb) strains during infection. In the laboratory Mtb strain H37Rv, the icl2 gene encodes two distinct gene products - Rv1915 and Rv1916 - due to a frameshift mutation. This study aims to characterise these two gene products to understand their structure and function. While we were unable to produce Rv1915 recombinantly, soluble Rv1916 was obtained with sufficient yield for characterisation. Kinetic studies using UV-visible spectrophotometry and ¹ H-NMR spectroscopy showed that recombinant Rv1916 does not possess isocitrate lyase activity, while waterLOGSY binding experiments demonstrated that it could bind acetyl-CoA. Finally, X-ray crystallography revealed structural similarities between Rv1916 and the C-terminal domain of ICL2. Considering the probable differences between full-length ICL2 and the gene products Rv1915 and Rv1916, care must be taken when using Mtb H37Rv as a model organism to study central carbon metabolism.

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Organizational Affiliation: 
• School of Chemistry and the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Rd, Parkville, VIC 3052, Australia.
School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
Present address: Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
Present address: Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.27 kDa 
• Atom Count: 1,461 
• Modeled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative isocitrate lyase subunit B	A	162	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: aceAb, Rv1916, RVBD_1916, LH57_10435, P425_01981 EC: 4.1.3.1
UniProt
Find proteins for O07717 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O07717  Go to UniProtKB:  O07717

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.046	α = 90
b = 86.046	β = 90
c = 73.586	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Kwai, B.X.C., Bashiri, G., Leung, I.K.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-07-26
  Changes: Database references
• Version 1.2: 2024-05-22
  Changes: Data collection