7ZD3 | pdb_00007zd3

Crystal structure of Pseudomonas aeruginosa S-adenosyl-L-homocysteine hydrolase inhibited by Zn2+ ions

PDB DOI: https://doi.org/10.2210/pdb7ZD3/pdb

Classification: HYDROLASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-29 Released: 2023-04-19
Deposition Author(s): Malecki, P.H., Gawel, M., Brzezinski, K.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.222 (Depositor), 0.223 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A closer look at molecular mechanisms underlying inhibition of S -adenosyl-L-homocysteine hydrolase by transition metal cations.

Gawel, M., Malecki, P.H., Sliwiak, J., Stepniewska, M., Imiolczyk, B., Czyrko-Horczak, J., Jakubczyk, D., Marczak, L., Plonska-Brzezinska, M.E., Brzezinski, K.

(2024) Chem Commun (Camb) 60: 11504-11507

PubMed: 39230573 Search on PubMed
DOI: https://doi.org/10.1039/d4cc03143a
Primary Citation Related Structures:
7ZD0, 7ZD1, 7ZD2, 7ZD3, 7ZD4

PubMed Abstract:
We report biochemical and structural studies on inhibiting bacterial S -adenosyl-L-homocysteine hydrolase by transition metal cations. Our results revealed diverse molecular mechanisms of enzyme inactivation. Depending on the cation, the mechanism is based on arresting the enzyme in its closed, inactive conformation, disulfide bond formation within the active site or oxidation of the intermediate form of a cofactor.

Organizational Affiliation

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland. kbrzezinski@ibch.poznan.pl.

Macromolecule Content

Total Structure Weight: 213.17 kDa
Atom Count: 16,660
Modeled Residue Count: 1,842
Deposited Residue Count: 1,888
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D	472	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: ahcY, sahH, PA0432 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q9I685 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I685 Go to UniProtKB: Q9I685
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I685
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain KA [auth D] SDF format, chain P [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain P [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain P [auth B]	AA [auth C], E [auth A], KA [auth D], P [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B]
ADN (Subject of Investigation/LOI) Query on ADN Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain F [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B]	BA [auth C], F [auth A], LA [auth D], Q [auth B]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Focus chain F [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain BA [auth C] Focus chain F [auth A] Focus chain LA [auth D] Focus chain Q [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
BCN Query on BCN Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain Y [auth B]	Y [auth B]	BICINE C₆ H₁₃ N O₄ FSVCELGFZIQNCK-UHFFFAOYSA-N		Interactions Focus chain Y [auth B] Interactions & Density Focus chain Y [auth B]
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain Z [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain Z [auth C]	EA [auth C], Z [auth C]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain Z [auth C] Interactions & Density Focus chain EA [auth C] Focus chain Z [auth C]
BU1 Query on BU1 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	G [auth A], H [auth A], J [auth A], R [auth B], S [auth B]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B]
PDO Query on PDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain FA [auth C]	CA [auth C], DA [auth C], FA [auth C]	1,3-PROPANDIOL C₃ H₈ O₂ YPFDHNVEDLHUCE-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth C] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] 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 OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] 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 OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] 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 OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	HA [auth C] IA [auth C] JA [auth C] L [auth A] M [auth A] HA [auth C], IA [auth C], JA [auth C], L [auth A], M [auth A], N [auth A], NA [auth D], O [auth A], OA [auth D], PA [auth D], QA [auth D], RA [auth D], U [auth B], V [auth B], W [auth B], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] 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 OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] 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 OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain K [auth A] SDF format, chain MA [auth D] SDF format, chain T [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain T [auth B]	GA [auth C], K [auth A], MA [auth D], T [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain K [auth A] Focus chain MA [auth D] Focus chain T [auth B] Interactions & Density Focus chain GA [auth C] Focus chain K [auth A] Focus chain MA [auth D] Focus chain T [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain SA [auth D] MOL2 format, chain SA [auth D] mmCIF format, chain SA [auth D]	SA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain SA [auth D] Interactions & Density Focus chain SA [auth D]