Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 24.25 kDa 
• Atom Count: 2035 
• Modelled Residue Count: 213 
• Deposited Residue Count: 217 
• Unique protein chains: 1

4NTZ

Crystal structure of Adenylate kinase from Streptococcus pneumoniae

• PDB DOI: 10.2210/pdb4NTZ/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae D39
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-03 Released: 2014-07-23 
• Deposition Author(s): Thach, T.T., Luong, T.T., Lee, S.H., Rhee, D.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Adenylate kinase from Streptococcus pneumoniae is essential for growth through its catalytic activity

Thach, T.T., Luong, T.T., Lee, S.H., Rhee, D.K.

(2014) FEBS Open Bio 4: 672-682

• PubMed: 25180151 
• DOI: 10.1016/j.fob.2014.07.002
• Primary Citation of Related Structures:  
  4NTZ, 4NU0


• PubMed Abstract: 
  

Streptococcus pneumoniae (pneumococcus) infection causes more than 1.6 million deaths worldwide. Pneumococcal growth is a prerequisite for its virulence and requires an appropriate supply of cellular energy. Adenylate kinases constitute a major family of enzymes that regulate cellular ATP levels. Some bacterial adenylate kinases (AdKs) are known to be critical for growth, but the physiological effects of AdKs in pneumococci have been poorly understood at the molecular level. Here, by crystallographic and functional studies, we report that the catalytic activity of adenylate kinase from S . pneumoniae (SpAdK) serotype 2 D39 is essential for growth. We determined the crystal structure of SpAdK in two conformations: ligand-free open form and closed in complex with a two-substrate mimic inhibitor adenosine pentaphosphate (Ap5A). Crystallographic analysis of SpAdK reveals Arg-89 as a key active site residue. We generated a conditional expression mutant of pneumococcus in which the expression of the adk gene is tightly regulated by fucose. The expression level of adk correlates with growth rate. Expression of the wild-type adk gene in fucose-inducible strains rescued a growth defect, but expression of the Arg-89 mutation did not. SpAdK increased total cellular ATP levels. Furthermore, lack of functional SpAdK caused a growth defect in vivo. Taken together, our results demonstrate that SpAdK is essential for pneumococcal growth in vitro and in vivo.

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Organizational Affiliation: 

School of Pharmacy, Sungkyunkwan University, Suwon 440-746, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A	217	Streptococcus pneumoniae D39	Mutation(s): 0  Gene Names: adk, SPD_0214 EC: 2.7.4.3
UniProt
Find proteins for Q04ML5 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04ML5  Go to UniProtKB:  Q04ML5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.22	α = 90
b = 53.7	β = 114.46
c = 50.87	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-03 
• Released Date: 2014-07-23 
Deposition Author(s): Thach, T.T., Luong, T.T., Lee, S.H., Rhee, D.K.

Revision History  

• Version 1.0: 2014-07-23
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references