6MDF | pdb_00006mdf

Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalonate bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural insight into substrate and product binding in an archaeal mevalonate kinase.

Miller, B.R.Kung, Y.

(2018) PLoS One 13: e0208419-e0208419

  • DOI: https://doi.org/10.1371/journal.pone.0208419
  • Primary Citation Related Structures: 
    6MDE, 6MDF

  • PubMed Abstract: 

    Mevalonate kinase (MK) is a key enzyme of the mevalonate pathway, which produces the biosynthetic precursors for steroids, including cholesterol, and isoprenoids, the largest class of natural products. Currently available crystal structures of MK from different organisms depict the enzyme in its unbound, substrate-bound, and inhibitor-bound forms; however, until now no structure has yet been determined of MK bound to its product, 5-phosphomevalonate. Here, we present crystal structures of mevalonate-bound and 5-phosphomevalonate-bound MK from Methanosarcina mazei (MmMK), a methanogenic archaeon. In contrast to the prior structure of a eukaryotic MK bound with mevalonate, we find a striking lack of direct interactions between this archaeal MK and its substrate. Further, these two MmMK structures join the prior structure of the apoenzyme to complete the first suite of structural snapshots that depict unbound, substrate-bound, and product-bound forms of the same MK. With this collection of structures, we now provide additional insight into the catalytic mechanism of this biologically essential enzyme.


  • Organizational Affiliation
    • Department of Chemistry, Bryn Mawr College, Bryn Mawr, PA, United States of America.

Macromolecule Content 

  • Total Structure Weight: 64.93 kDa 
  • Atom Count: 4,659 
  • Modeled Residue Count: 604 
  • Deposited Residue Count: 606 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mevalonate kinase
A, B
303Methanosarcina mazeiMutation(s): 0 
Gene Names: mvkMM_1762
EC: 2.7.1.36
UniProt
Find proteins for Q8PW39 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88))
Explore Q8PW39 
Go to UniProtKB:  Q8PW39
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PW39
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PMV
(Subject of Investigation/LOI)

Query on PMV



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
(3R)-3-HYDROXY-3-METHYL-5-(PHOSPHONOOXY)PENTANOIC ACID
C6 H13 O7 P
OKZYCXHTTZZYSK-ZCFIWIBFSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.97α = 90
b = 58.581β = 90
c = 190.03γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM116029

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description