1MKY | pdb_00001mky

Structural Analysis of the Domain Interactions in Der, a Switch Protein Containing Two GTPase Domains

• PDB DOI: https://doi.org/10.2210/pdb1MKY/pdb

• Classification: LIGAND BINDING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-08-29 Released: 2003-01-14 
• Deposition Author(s): Robinson, V.L., Hwang, J., Fox, E., Inouye, M., Stock, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.204 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Domain Arrangement of Der, a Switch Protein Containing Two GTPase Domains

Robinson, V.L., Hwang, J., Fox, E., Inouye, M., Stock, A.M.

(2002) Structure 10: 1649-1658

• PubMed: 12467572 
• DOI: https://doi.org/10.1016/s0969-2126(02)00905-x
• Primary Citation Related Structures: 
  1MKY


• PubMed Abstract: 
  

  The EngA subfamily of essential bacterial GTPases has a unique domain structure consisting of two adjacent GTPase domains (GD1 and GD2) and a C-terminal domain. The structure of Thermotoga maritima Der bound to GDP determined at 1.9 A resolution reveals a novel domain arrangement in which the GTPase domains pack at either side of the C-terminal domain. Unexpectedly, the C-terminal domain resembles a KH domain, missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2.

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Organizational Affiliation: 
• Howard Hughes Medical Institute and Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.46 kDa 
• Atom Count: 3,563 
• Modeled Residue Count: 407 
• Deposited Residue Count: 439 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable GTP-binding protein engA	A	439	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9X1F8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1F8  Go to UniProtKB:  Q9X1F8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	G [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.204 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.137	α = 90
b = 77.994	β = 90
c = 96.597	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-14 
Deposition Author(s): Robinson, V.L., Hwang, J., Fox, E., Inouye, M., Stock, A.M.

Revision History  

• Version 1.0: 2003-01-14
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2015-02-04
  Changes: Database references, Other
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary