8IDU | pdb_00008idu

Crystal structure of substrate bound-form dehydroquinate dehydratase from Corynebacterium glutamicum

PDB DOI: https://doi.org/10.2210/pdb8IDU/pdb

Classification: LYASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2023-02-14 Released: 2023-12-27
Deposition Author(s): Lee, C.H., Kim, S., Kim, K.-J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.169 (Depositor), 0.176 (DCC)
R-Value Work:
0.142 (Depositor), 0.154 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Biochemical Analysis of 3-Dehydroquinate Dehydratase from Corynebacterium glutamicum .

Lee, C.H., Kim, S., Seo, H., Kim, K.J.

(2023) J Microbiol Biotechnol 33: 1595-1605

PubMed: 38151830 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.4014/jmb.2305.05018
Primary Citation Related Structures:
8IDR, 8IDU

PubMed Abstract:
Dehydroquinate dehydratase (DHQD) catalyzes the conversion of 3-dehydroquinic acid (DHQ) into 3-dehydroshikimic acid in the mid stage of the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids and folates. Here, we report two the crystal structures of type II DHQD ( Cg DHQD) derived from Corynebacterium glutamicum , which is a widely used industrial platform organism. We determined the structures for Cg DHQD ^WT with the citrate at a resolution of 1.80Å and Cg DHQD ^R19A with DHQ complexed forms at a resolution of 2.00 Å, respectively. The enzyme forms a homododecamer consisting of four trimers with three interfacial active sites. We identified the DHQ-binding site of Cg DHQD and observed an unusual binding mode of citrate inhibitor in the site with a half-opened lid loop. A structural comparison of Cg DHQD with a homolog derived from Streptomyces coelicolor revealed differences in the terminal regions, lid loop, and active site. Particularly, Cg DHQD, including some Corynebacterium species, possesses a distinctive residue P105, which is not conserved in other DHQDs at the position near the 5-hydroxyl group of DHQ. Replacements of P105 with isoleucine and valine, conserved in other DHQDs, caused an approximately 70% decrease in the activity, but replacement of S103 with threonine ( Cg DHQD ^S103T) caused a 10% increase in the activity. Our biochemical studies revealed the importance of key residues and enzyme kinetics for wild type and Cg DHQD ^S103T, explaining the effect of the variation. This structural and biochemical study provides valuable information for understanding the reaction efficiency that varies due to structural differences caused by the unique sequences of Cg DHQD.

Organizational Affiliation

School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.

Macromolecule Content

Total Structure Weight: 101.56 kDa
Atom Count: 7,409
Modeled Residue Count: 858
Deposited Residue Count: 918
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B, C, D, E A, B, C, D, E, F	153	Corynebacterium glutamicum ATCC 13032	Mutation(s): 1 Gene Names: aroQ, aroD, Cgl0423, cg0503 EC: 4.2.1.10
UniProt
Find proteins for O52377 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore O52377 Go to UniProtKB: O52377
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O52377
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DQA (Subject of Investigation/LOI) Query on DQA Download:Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain CA [auth F] MOL2 format, chain W [auth E] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain CA [auth F] mmCIF format, chain W [auth E] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain CA [auth F]	CA [auth F] I [auth A] L [auth B] Q [auth C] U [auth D] CA [auth F], I [auth A], L [auth B], Q [auth C], U [auth D], W [auth E]	1,3,4-TRIHYDROXY-5-OXO-CYCLOHEXANECARBOXYLIC ACID C₇ H₁₀ O₆ WVMWZWGZRAXUBK-SYTVJDICSA-N		Interactions Focus chain CA [auth F] Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E] Interactions & Density Focus chain CA [auth F] Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain W [auth E]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] G [auth A] H [auth A] O [auth C] AA [auth F], BA [auth F], G [auth A], H [auth A], O [auth C], S [auth D], T [auth D], Y [auth F], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain Y [auth F] Focus chain Z [auth F]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain X [auth E] SDF format, chain R [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain DA [auth F] MOL2 format, chain V [auth D] MOL2 format, chain X [auth E] MOL2 format, chain R [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain DA [auth F] mmCIF format, chain V [auth D] mmCIF format, chain X [auth E] mmCIF format, chain R [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain DA [auth F]	DA [auth F] J [auth A] K [auth A] M [auth B] N [auth B] DA [auth F], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], R [auth C], V [auth D], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain X [auth E] Interactions & Density Focus chain DA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain X [auth E]