1UQR | pdb_00001uqr

Type II 3-dehydroquinate dehydratase (DHQase) from Actinobacillus pleuropneumoniae

PDB DOI: https://doi.org/10.2210/pdb1UQR/pdb

Classification: LYASE
Organism(s): Actinobacillus pleuropneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-10-16 Released: 2003-10-30
Deposition Author(s): Maes, D., Gonzalez-Ramirez, L.A., Lopez-Jaramillo, J., Yu, B., De Bondt, H., Zegers, I., Afonina, E., Garcia-Ruiz, J.M., Gulnik, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.199 (Depositor), 0.193 (DCC)
R-Value Work:
0.178 (Depositor), 0.173 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural Study of the Type II 3-Dehydroquinate Dehydratase from Actinobacillus Pleuropneumoniae

Maes, D., Gonzalez-Ramirez, L.A., Lopez-Jaramillo, J., Yu, B., De Bondt, H., Zegers, I., Afonina, E., Garcia-Ruiz, J.M., Gulnik, S.

(2004) Acta Crystallogr D Biol Crystallogr 60: 463

PubMed: 14993670 Search on PubMed
DOI: https://doi.org/10.1107/S090744490302969X
Primary Citation Related Structures:
1UQR

PubMed Abstract:
The structure of the type II dehydroquinate dehydratase (DHQase) from Actinobacillus pleuropneumoniae, the third enzyme of the shikimate pathway, has been determined. Crystals diffracting to 1.7 A were obtained in space and on earth using the counter-diffusion technique. The structure was solved using molecular replacement and refined to high resolution. The overall structure of the dodecameric enzyme is described and compared with structures of DHQases from other bacteria. DHQases contain a flexible loop that presumably closes over the active site upon substrate binding. The enzyme can exist in an open or closed conformation. The present structure displays the open conformation, with a sulfate anion bound in the active site. The availability of this structure opens a route to structure-based antibiotics targetting this pathogenic bacterium.

Organizational Affiliation

ULTR, Vrije Universiteit Brussel, Vlaams Interuniversitair Instituut voor Biotechnologie (VIB), Pleinlaan 2, 1050 Brussels, Belgium. dominique.maes@vub.ac.be

Macromolecule Content

Total Structure Weight: 209.84 kDa
Atom Count: 16,147
Modeled Residue Count: 1,738
Deposited Residue Count: 1,848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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, G, H, I, J, K, L	154	Actinobacillus pleuropneumoniae	Mutation(s): 0 EC: 4.2.1.10
UniProt
Find proteins for P43877 (Actinobacillus pleuropneumoniae) Explore P43877 Go to UniProtKB: P43877
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43877
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain SA [auth K] SDF format, chain Q [auth B] SDF format, chain KA [auth H] SDF format, chain AA [auth E] MOL2 format, chain SA [auth K] MOL2 format, chain Q [auth B] MOL2 format, chain KA [auth H] MOL2 format, chain AA [auth E] mmCIF format, chain SA [auth K] mmCIF format, chain Q [auth B] mmCIF format, chain KA [auth H] mmCIF format, chain AA [auth E]	AA [auth E], KA [auth H], Q [auth B], SA [auth K]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain AA [auth E] Focus chain KA [auth H] Focus chain Q [auth B] Focus chain SA [auth K] Interactions & Density Focus chain AA [auth E] Focus chain KA [auth H] Focus chain Q [auth B] Focus chain SA [auth K]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain UA [auth L] SDF format, chain U [auth D] SDF format, chain TA [auth L] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain RA [auth K] SDF format, chain R [auth C] SDF format, chain QA [auth K] SDF format, chain PA [auth K] SDF format, chain P [auth B] SDF format, chain OA [auth J] SDF format, chain O [auth B] SDF format, chain NA [auth J] SDF format, chain N [auth A] SDF format, chain MA [auth J] SDF format, chain M [auth A] SDF format, chain LA [auth I] SDF format, chain JA [auth H] SDF format, chain IA [auth H] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain FA [auth G] SDF format, chain EA [auth F] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain BA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain UA [auth L] MOL2 format, chain U [auth D] MOL2 format, chain TA [auth L] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth K] MOL2 format, chain R [auth C] MOL2 format, chain QA [auth K] MOL2 format, chain PA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain UA [auth L] mmCIF format, chain U [auth D] mmCIF format, chain TA [auth L] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth K] mmCIF format, chain R [auth C] mmCIF format, chain QA [auth K] mmCIF format, chain PA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain NA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F]	BA [auth F] CA [auth F] DA [auth F] EA [auth F] FA [auth G] BA [auth F], CA [auth F], DA [auth F], EA [auth F], FA [auth G], GA [auth H], HA [auth H], IA [auth H], JA [auth H], LA [auth I], M [auth A], MA [auth J], N [auth A], NA [auth J], O [auth B], OA [auth J], P [auth B], PA [auth K], QA [auth K], R [auth C], RA [auth K], S [auth C], T [auth C], TA [auth L], U [auth D], UA [auth L], V [auth D], W [auth D], X [auth E], Y [auth E], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain R [auth C] Focus chain RA [auth K] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth L] Focus chain U [auth D] Focus chain UA [auth L] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth J] Focus chain O [auth B] Focus chain OA [auth J] Focus chain P [auth B] Focus chain PA [auth K] Focus chain QA [auth K] Focus chain R [auth C] Focus chain RA [auth K] Focus chain S [auth C] Focus chain T [auth C] Focus chain TA [auth L] Focus chain U [auth D] Focus chain UA [auth L] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.199 (Depositor), 0.193 (DCC)
R-Value Work: 0.178 (Depositor), 0.173 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.095	α = 90
b = 131.333	β = 90
c = 161.619	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-10-30

Deposition Author(s):

Maes, D.

Gonzalez-Ramirez, L.A.

Revision History (Full details and data files)

Version 1.0: 2003-10-30
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-07-24
Changes: Data collection
Version 1.4: 2024-05-08
Changes: Data collection, Database references, Other