2OI2

Streptococcus pneumoniae Mevalonate Kinase in Complex with Diphosphomevalonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the Streptococcus pneumoniae mevalonate kinase in complex with diphosphomevalonate.

Andreassi, J.L.Bilder, P.W.Vetting, M.W.Roderick, S.L.Leyh, T.S.

(2007) Protein Sci 16: 983-989

  • DOI: 10.1110/ps.072755707
  • Primary Citation of Related Structures:  
    2OI2

  • PubMed Abstract: 
  • Streptococcus pneumoniae, a ubiquitous gram-positive pathogen with an alarming, steadily evolving resistance to frontline antimicrobials, poses a severe global health threat both in the community and in the clinic. The recent discovery that diphosphomevalonate (DPM), an essential intermediate in the isoprenoid biosynthetic pathway, potently and allosterically inhibits S ...

    Streptococcus pneumoniae, a ubiquitous gram-positive pathogen with an alarming, steadily evolving resistance to frontline antimicrobials, poses a severe global health threat both in the community and in the clinic. The recent discovery that diphosphomevalonate (DPM), an essential intermediate in the isoprenoid biosynthetic pathway, potently and allosterically inhibits S. pneumoniae mevalonate kinase (SpMK) without affecting the human isozyme established a new target and lead compound for antimicrobial design. Here we present the crystal structure of the first S. pneumoniae mevalonate kinase, at a resolution of 2.5 A and in complex with DPM.Mg(2+) in the active-site cleft. Structural comparison of SpMK with other members of the GHMP kinase family reveals that DPM functions as a partial bisubstrate analog (mevalonate linked to the pyrophosphoryl moiety of ATP) in that it elicits a ternary-complexlike form of the enzyme, except for localized disordering in a region that would otherwise interact with the missing portion of the nucleotide. Features of the SpMK-binding pockets are discussed in the context of established mechanistic findings and inherited human diseases linked to MK deficiency.


    Organizational Affiliation

    DuPont Crop Protection, Stine-Haskell Research Center, Newark, Delaware 19711, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mevalonate kinaseA292Streptococcus pneumoniaeMutation(s): 0 
Gene Names: mvk
EC: 2.7.1.36
UniProt
Find proteins for A0A0H2UNK6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2UNK6 
Go to UniProtKB:  A0A0H2UNK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2UNK6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DP6
Query on DP6

Download Ideal Coordinates CCD File 
C [auth A](3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID
C6 H14 O10 P2
SIGQQUBJQXSAMW-ZCFIWIBFSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DP6 PDBBind:  2OI2 Kd: 500 (nM) from 1 assay(s)
Binding MOAD:  2OI2 Kd: 500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.597α = 90
b = 101.597β = 90
c = 83.28γ = 120
Software Package:
Software NamePurpose
CNSrefinement
CTRdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance