3T5C | pdb_00003t5c

Crystal structure of N-terminal domain of FACL13 from Mycobacterium tuberculosis in different space group C2

• PDB DOI: https://doi.org/10.2210/pdb3T5C/pdb

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


• Deposited: 2011-07-27 Released: 2012-01-25 
• Deposition Author(s): Goyal, A., Sankaranarayanan, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.263 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Molecular basis of the functional divergence of fatty acyl-AMP ligase biosynthetic enzymes of Mycobacterium tuberculosis.

Goyal, A., Verma, P., Anandhakrishnan, M., Gokhale, R.S., Sankaranarayanan, R.

(2012) J Mol Biology 416: 221-238

• PubMed: 22206988 
• DOI: https://doi.org/10.1016/j.jmb.2011.12.031
• Primary Citation Related Structures: 
  3T5A, 3T5B, 3T5C


• PubMed Abstract: 
  

  Activation of fatty acids as acyl-adenylates by fatty acyl-AMP ligases (FAALs) in Mycobacterium tuberculosis is a variant of a classical theme that involves formation of acyl-CoA (coenzyme A) by fatty acyl-CoA ligases (FACLs). Here, we show that FAALs and FACLs possess similar structural fold and substrate specificity determinants, and the key difference is the absence of a unique insertion sequence in FACL13 structure. A systematic analysis shows a conserved hydrophobic anchorage of the insertion motif across several FAALs. Strikingly, mutagenesis of two phenylalanine residues, which are part of the anchorage, to alanine converts FAAL32 to FACL32. This insertion-based in silico analysis suggests the presence of FAAL homologues in several other non-mycobacterial genomes including eukaryotes. The work presented here establishes an elegant mechanism wherein an insertion sequence drives the functional divergence of FAALs from canonical FACLs.

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Organizational Affiliation: 
• Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad 500 007, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 85.68 kDa 
• Atom Count: 6,461 
• Modeled Residue Count: 784 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE CHAIN-FATTY-ACID-CoA LIGASE FADD13	A, B	396	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: fadD13, MT3174, Rv3089 EC: 6.2.1 (PDB Primary Data), 6.2.1.3 (UniProt)
UniProt
Find proteins for P9WQ37 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WQ37  Go to UniProtKB:  P9WQ37

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.263 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.228	α = 90
b = 91.983	β = 130.79
c = 84.412	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Goyal, A., Sankaranarayanan, R.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description