1G3R | pdb_00001g3r

CRYSTAL STRUCTURE ANALYSIS OF PYROCOCCUS FURIOSUS CELL DIVISION ATPASE MIND

• PDB DOI: https://doi.org/10.2210/pdb1G3R/pdb

• Classification: cell cycle, hydrolase
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2000-10-25 Released: 2001-04-21 
• Deposition Author(s): Hayashi, I., Oyama, T., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus.

Hayashi, I., Oyama, T., Morikawa, K.

(2001) EMBO J 20: 1819-1828

• PubMed: 11296216 
• DOI: https://doi.org/10.1093/emboj/20.8.1819
• Primary Citation Related Structures: 
  1G3Q, 1G3R


• PubMed Abstract: 
  

  Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. To clarify the functional role of the bacterial cell division inhibitor MinD, which is a membrane-associated ATPase that works as an activator of MinC, we determined the crystal structure of a Pyrococcus furiosus MinD homologue complexed with a substrate analogue, AMPPCP, and with the product ADP at resolutions of 2.7 and 2.0 A, respectively. The structure reveals general similarities to the nitrogenase iron protein, the H-Ras p21 and the RecA-like ATPase domain. Alanine scanning mutational analyses of E.coli MinD were also performed in vivo. The results suggest that the residues around the ATP-binding site are required for the direct interaction with MinC, and that ATP binding and hydrolysis play a role as a molecular switch to control the mechanisms of MinCDE-dependent bacterial cell division.

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Organizational Affiliation: 
• Department of Structural Biology, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita-City, Osaka 565-0874, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 25.86 kDa 
• Atom Count: 1,876 
• Modeled Residue Count: 237 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION INHIBITOR	A	237	Pyrococcus furiosus	Mutation(s): 0  Gene Names: MIND
UniProt
Find proteins for Q8U3I1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U3I1  Go to UniProtKB:  Q8U3I1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP	C [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Work:  0.209 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.644	α = 90
b = 98.644	β = 90
c = 98.644	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-04-21 
Deposition Author(s): Hayashi, I., Oyama, T., Morikawa, K.

Revision History  

• Version 1.0: 2001-04-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations