4G9P | pdb_00004g9p

Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus

PDB DOI: https://doi.org/10.2210/pdb4G9P/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB27
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-07-24 Released: 2012-09-26
Deposition Author(s): Rekittke, I., Jomaa, H., Ermler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.203 (Depositor), 0.202 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of the GcpE (IspG)-MEcPP complex from Thermus thermophilus.

Rekittke, I., Jomaa, H., Ermler, U.

(2012) FEBS Lett 586: 3452-3457

PubMed: 22967895 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2012.07.070
Primary Citation Related Structures:
4G9P

PubMed Abstract:
Isoprenoid precursor biosynthesis occurs through the mevalonate or the methylerythritol phosphate (MEP) pathway, used i.e., by humans and by many human pathogens, respectively. In the MEP pathway, 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate (MEcPP) is converted to (E)-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (HMBPP) by the iron-sulfur cluster enzyme HMBPP synthase (GcpE). The presented X-ray structure of the GcpE-MEcPP complex from Thermus thermophilus at 1.55Å resolution provides valuable information about the catalytic mechanism and for rational inhibitor design. MEcPP binding inside the TIM-barrel funnel induces a 60° rotation of the [4Fe-4S] cluster containing domain onto the TIM-barrel entrance. The apical iron of the [4Fe-4S] cluster ligates with the C3 oxygen atom of MEcPP.

Organizational Affiliation

Institut für Klinische Immunologie und Transfusionsmedizin, Justus-Liebig-Universität Giessen, Giessen, Germany.

Macromolecule Content

Total Structure Weight: 45.41 kDa
Atom Count: 3,656
Modeled Residue Count: 405
Deposited Residue Count: 406
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase	A	406	Thermus thermophilus HB27	Mutation(s): 0 Gene Names: gcpE, ispG, TT_C1677 EC: 1.17.7.1 (PDB Primary Data), 1.17.7.3 (UniProt)
UniProt
Find proteins for Q72H18 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72H18 Go to UniProtKB: Q72H18
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72H18
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CDI Query on CDI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE C₅ H₁₂ O₉ P₂ SFRQRNJMIIUYDI-UHNVWZDZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A]	D [auth A], G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain G [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A]	E [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.203 (Depositor), 0.202 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.65	α = 90
b = 63.65	β = 90
c = 442.27	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Rekittke, I.

Jomaa, H.

Ermler, U.

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2012-10-17
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations