2CDN | pdb_00002cdn

Crystal structure of Mycobacterium tuberculosis adenylate kinase complexed with two molecules of ADP and Mg

• PDB DOI: https://doi.org/10.2210/pdb2CDN/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-25 Released: 2006-05-10 
• Deposition Author(s): Bellinzoni, M., Haouz, A., Grana, M., Munier-Lehmann, H., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Mycobacterium Tuberculosis Adenylate Kinase in Complex with Two Molecules of Adp and Mg2+ Supports an Associative Mechanism for Phosphoryl Transfer.

Bellinzoni, M., Haouz, A., Grana, M., Munier-Lehmann, H., Shepard, W., Alzari, P.M.

(2006) Protein Sci 15: 1489

• PubMed: 16672241 
• DOI: https://doi.org/10.1110/ps.062163406
• Primary Citation Related Structures: 
  2CDN


• PubMed Abstract: 
  

  The crystal structure of Mycobacterium tuberculosis adenylate kinase (MtAK) in complex with two ADP molecules and Mg2+ has been determined at 1.9 A resolution. Comparison with the solution structure of the enzyme, obtained in the absence of substrates, shows significant conformational changes of the LID and NMP-binding domains upon substrate binding. The ternary complex represents the state of the enzyme at the start of the backward reaction (ATP synthesis). The structure is consistent with a direct nucleophilic attack of a terminal oxygen from the acceptor ADP molecule on the beta-phosphate from the donor substrate, and both the geometry and the distribution of positive charge in the active site support the hypothesis of an associative mechanism for phosphoryl transfer.

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Organizational Affiliation: 
• Unité de Biochimie Structurale, CNRS-URA 2185, Institut Pasteur, F-75724 Paris, France.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 23.2 kDa 
• Atom Count: 1,624 
• Modeled Residue Count: 186 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENYLATE KINASE	A	201	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 2.7.4.3
UniProt
Find proteins for P9WKF5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKF5  Go to UniProtKB:  P9WKF5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.544	α = 90
b = 64.91	β = 110.12
c = 39.773	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-10 
Deposition Author(s): Bellinzoni, M., Haouz, A., Grana, M., Munier-Lehmann, H., Alzari, P.M.

Revision History  

• Version 1.0: 2006-05-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description