5T8U | pdb_00005t8u

Crystal structure of P. falciparum LipL1 in complex lipoate

• PDB DOI: https://doi.org/10.2210/pdb5T8U/pdb

• Classification: LIGASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-08 Released: 2017-05-31 
• Deposition Author(s): Guerra, A.J., Afanador, G.A., Prigge, S.T.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.302 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of lipoate-bound lipoate ligase 1, LipL1, from Plasmodium falciparum.

Guerra, A.J., Afanador, G.A., Prigge, S.T.

(2017) Proteins 85: 1777-1783

• PubMed: 28543853 
• DOI: https://doi.org/10.1002/prot.25324
• Primary Citation of Related Structures:  
  5T8U


• PubMed Abstract: 
  

  Plasmodium falciparum lipoate protein ligase 1 (PfLipL1) is an ATP-dependent ligase that belongs to the biotin/lipoate A/B protein ligase family (PFAM PF03099). PfLipL1 is the only known canonical lipoate ligase in Pf and functions as a redox switch between two lipoylation routes in the parasite mitochondrion. Here, we report the crystal structure of a deletion construct of PfLipL1 (PfLipL1 _Δ243-279 ) bound to lipoate, and validate the lipoylation activity of this construct in both an in vitro lipoylation assay and a cell-based lipoylation assay. This characterization represents the first step in understanding the redox dependence of the lipoylation mechanism in malaria parasites. Proteins 2017; 85:1777-1783. © 2017 Wiley Periodicals, Inc.

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Organizational Affiliation: 

Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84.82 kDa 
• Atom Count: 5,594 
• Modelled Residue Count: 669 
• Deposited Residue Count: 720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoate-protein ligase 1	A, B	360	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF3D7_1314600 EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt)
UniProt
Find proteins for Q8IEG9 (Plasmodium falciparum (isolate 3D7)) Explore Q8IEG9  Go to UniProtKB:  Q8IEG9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LPA	C [auth A], D [auth B]	LIPOIC ACID C8 H14 O2 S2 AGBQKNBQESQNJD-SSDOTTSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.302 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.24	α = 90
b = 120.24	β = 90
c = 134.92	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Guerra, A.J., Afanador, G.A., Prigge, S.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI065853
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	F32 AI110028

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2017-09-06
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2023-10-04
  Changes: Data collection, Database references, Refinement description