3HWW

Crystal structure of menaquinone synthesis protein MenD from E. coli in complex with oxoglutarate

PDB DOI: https://doi.org/10.2210/pdb3HWW/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-06-19 Released: 2009-11-03
Deposition Author(s): Priyadarshi, A., Hwang, K.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.255
R-Value Work: 0.209
R-Value Observed: 0.211

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural and functional analysis of Vitamin K2 synthesis protein MenD.

Priyadarshi, A., Kim, E.E., Hwang, K.Y.

(2009) Biochem Biophys Res Commun 388: 748-751

PubMed: 19703421 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2009.08.093
Primary Citation of Related Structures:
3HWW, 3HWX

PubMed Abstract:
Here we describe in detail the crystal structures of the Vitamin K(2) synthesis protein MenD, from Escherichia coli, in complex with thiamine diphosphate (ThDP) and oxoglutarate, and the effects of cofactor and substrate on its structural stability. This is the first reported structure of MenD in complex with oxoglutarate. The residues Gly472 to Phe488 of the active site region are either disordered, or in an open conformation in the MenD oxoglutarate complex structure, but adopt a closed conformation in the MenD ThDP complex structure. Biospecific-interaction analysis using surface plasmon resonance (SPR) technology reveals an affinity for ThDP and oxoglutarate in the nanomolar range. Biochemical and structural analysis confirmed that MenD is highly dependent on ThDP for its structural stability. Our structural results combined with the biochemical assay reveal novel features of the enzyme that could be utilized in a program of rational structure-based drug design, as well as in helping to enhance our knowledge of the menaquinone synthesis pathway in greater detail.

Organizational Affiliation

Biomedical Research Center, Korea Institute of Science and Technology, Seoul 136-791, South Korea.

Macromolecule Content

Total Structure Weight: 124.71 kDa
Atom Count: 8,750
Modelled Residue Count: 1,071
Deposited Residue Count: 1,112
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	A, B [auth D]	556	Escherichia coli K-12	Mutation(s): 1 Gene Names: b2264, JW5374, menD EC: 2.2.1.9
UniProt
Find proteins for P17109 (Escherichia coli (strain K12)) Explore P17109 Go to UniProtKB: P17109
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17109
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AKG Query on AKG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain AA [auth D] MOL2 format, chain C [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain C [auth A] mmCIF format, chain AA [auth D]	AA [auth D], C [auth A]	2-OXOGLUTARIC ACID C₅ H₆ O₅ KPGXRSRHYNQIFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain C [auth A] Interactions & Density Focus chain AA [auth D] Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain MA [auth D] SDF format, chain OA [auth D] SDF format, chain W [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain YA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain YA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain YA [auth D]	MA [auth D] OA [auth D] W [auth A] Y [auth A] YA [auth D] MA [auth D], OA [auth D], W [auth A], Y [auth A], YA [auth D], Z [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain MA [auth D] Focus chain OA [auth D] Focus chain W [auth A] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Interactions & Density Focus chain MA [auth D] Focus chain OA [auth D] Focus chain W [auth A] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain I [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain I [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain I [auth A]	I [auth A], LA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain LA [auth D] Interactions & Density Focus chain I [auth A] Focus chain LA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain BA [auth D] MOL2 format, chain D [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain D [auth A] mmCIF format, chain BA [auth D]	BA [auth D], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain D [auth A] Interactions & Density Focus chain BA [auth D] Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain HA [auth D] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain SA [auth D] SDF format, chain UA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain UA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain UA [auth D]	CA [auth D] DA [auth D] E [auth A] EA [auth D] F [auth A] CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], M [auth A], N [auth A], NA [auth D], O [auth A], P [auth A], PA [auth D], Q [auth A], QA [auth D], R [auth A], RA [auth D], S [auth A], SA [auth D], T [auth A], TA [auth D], U [auth A], UA [auth D], V [auth A], VA [auth D], WA [auth D], X [auth A], XA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain V [auth A] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Focus chain UA [auth D] Focus chain V [auth A] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
AKG	PDBBind: 3HWW	Kd: 75 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.255
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.91	α = 90
b = 117.91	β = 90
c = 175.276	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-03

Deposition Author(s):

Priyadarshi, A.

Hwang, K.Y.

Revision History (Full details and data files)

Version 1.0: 2009-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description