5YEI | pdb_00005yei

Mechanistic insight into the regulation of Pseudomonas aeruginosa aspartate kinase

PDB DOI: https://doi.org/10.2210/pdb5YEI/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-09-17 Released: 2018-08-29
Deposition Author(s): Li, C., Yang, M., Liu, L., Peng, C., Li, T., He, L., Song, Y., Zhu, Y., Bao, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.222 (Depositor), 0.223 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Mechanistic insights into the allosteric regulation of Pseudomonas aeruginosa aspartate kinase.

Li, C., Yang, M., Liu, L., Li, T., Peng, C., He, L., Song, Y., Zhu, Y., Shen, Y., Yang, J., Zhao, N., Zhao, C., Zhou, Q., Li, H., Kang, M., Tong, A., Tang, H., Bao, R.

(2018) Biochem J 475: 1107-1119

PubMed: 29382741 Search on PubMed
DOI: https://doi.org/10.1042/BCJ20170829
Primary Citation Related Structures:
5YEI

PubMed Abstract:
In plants and microorganisms, aspartate kinase (AK) catalyzes an initial commitment step of the aspartate family amino acid biosynthesis. Owing to various structural organizations, AKs from different species show tremendous diversity and complex allosteric controls. We report the crystal structure of AK from Pseudomonas aeruginosa (PaAK), a typical α2β2 hetero-tetrameric enzyme, in complex with inhibitory effectors. Distinctive features of PaAK are revealed by structural and biochemical analyses. Essentially, the open conformation of Lys-/Thr-bound PaAK structure clarifies the inhibitory mechanism of α2β2-type AK. Moreover, the various inhibitory effectors of PaAK have been identified and a general amino acid effector motif of AK family is described.

Organizational Affiliation

Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.

Macromolecule Content

Total Structure Weight: 250.57 kDa
Atom Count: 16,949
Modeled Residue Count: 2,207
Deposited Residue Count: 2,304
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	A [auth D], B, C [auth F], E [auth H]	164	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lysC, PA0904 EC: 2.7.2.4
UniProt
Find proteins for O69077 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore O69077 Go to UniProtKB: O69077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O69077
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartokinase	D [auth C], F [auth G], G [auth A], H [auth E]	412	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lysC, PA0904 EC: 2.7.2.4
UniProt
Find proteins for O69077 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore O69077 Go to UniProtKB: O69077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O69077
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain Q [auth G] SDF format, chain S [auth A] SDF format, chain W [auth E] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth G] MOL2 format, chain S [auth A] MOL2 format, chain W [auth E] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth G] mmCIF format, chain S [auth A] mmCIF format, chain W [auth E]	N [auth C], Q [auth G], S [auth A], W [auth E]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain N [auth C] Focus chain Q [auth G] Focus chain S [auth A] Focus chain W [auth E] Interactions & Density Focus chain N [auth C] Focus chain Q [auth G] Focus chain S [auth A] Focus chain W [auth E]
THR Query on THR Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain J [auth B] SDF format, chain K [auth F] SDF format, chain L [auth F] SDF format, chain M [auth C] SDF format, chain O [auth H] SDF format, chain R [auth G] SDF format, chain T [auth A] MOL2 format, chain I [auth D] MOL2 format, chain J [auth B] MOL2 format, chain K [auth F] MOL2 format, chain L [auth F] MOL2 format, chain M [auth C] MOL2 format, chain O [auth H] MOL2 format, chain R [auth G] MOL2 format, chain T [auth A] mmCIF format, chain I [auth D] mmCIF format, chain J [auth B] mmCIF format, chain K [auth F] mmCIF format, chain L [auth F] mmCIF format, chain M [auth C] mmCIF format, chain O [auth H] mmCIF format, chain R [auth G] mmCIF format, chain T [auth A]	I [auth D] J [auth B] K [auth F] L [auth F] M [auth C] I [auth D], J [auth B], K [auth F], L [auth F], M [auth C], O [auth H], R [auth G], T [auth A]	THREONINE C₄ H₉ N O₃ AYFVYJQAPQTCCC-GBXIJSLDSA-N		Interactions Focus chain I [auth D] Focus chain J [auth B] Focus chain K [auth F] Focus chain L [auth F] Focus chain M [auth C] Focus chain O [auth H] Focus chain R [auth G] Focus chain T [auth A] Interactions & Density Focus chain I [auth D] Focus chain J [auth B] Focus chain K [auth F] Focus chain L [auth F] Focus chain M [auth C] Focus chain O [auth H] Focus chain R [auth G] Focus chain T [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth G] SDF format, chain U [auth E] SDF format, chain V [auth E] MOL2 format, chain P [auth G] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] mmCIF format, chain P [auth G] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E]	P [auth G], U [auth E], V [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth G] Focus chain U [auth E] Focus chain V [auth E] Interactions & Density Focus chain P [auth G] Focus chain U [auth E] Focus chain V [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor), 0.257 (DCC)
R-Value Work: 0.222 (Depositor), 0.223 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.459	α = 90
b = 171.793	β = 90.29
c = 88.932	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-08-29
Type: Initial release
Version 1.1: 2019-09-11
Changes: Data collection, Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description