3IAF | pdb_00003iaf

Structure of benzaldehyde lyase A28S mutant with monomethyl benzoylphosphonate

PDB DOI: https://doi.org/10.2210/pdb3IAF/pdb

Classification: LYASE
Organism(s): Pseudomonas fluorescens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-07-13 Released: 2010-03-02
Deposition Author(s): Brandt, G.S., Petsko, G.A., Ringe, D., McLeish, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.260 (Depositor), 0.260 (DCC)
R-Value Work:
0.213 (Depositor), 0.211 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Active-site engineering of benzaldehyde lyase shows that a point mutation can confer both new reactivity and susceptibility to mechanism-based inhibition.

Brandt, G.S., Kneen, M.M., Petsko, G.A., Ringe, D., McLeish, M.J.

(2010) J Am Chem Soc 132: 438-439

PubMed: 20030408 Search on PubMed
DOI: https://doi.org/10.1021/ja907064w
Primary Citation Related Structures:
3IAE, 3IAF

PubMed Abstract:
Benzaldehyde lyase (BAL) from Pseudomonas putida is a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the breakdown of (R)-benzoin. Here we report that a point mutant, BAL A28S, not only catalyzes the decarboxylation of benzoylformate but, like benzoylformate decarboxylase (BFDC), is also inactivated by the benzoylformate analogues methyl benzoylphosphonate (MBP) and benzoylphosphonate (BP). The latter has no effect on wild-type BAL, and the inactivation of the A28S variant is shown to result from phosphorylation of the newly introduced serine residue. This lends support to the proposal that an appropriately placed nucleophile facilitates the expulsion of carbon dioxide from the active site in many ThDP-dependent decarboxylases.

Organizational Affiliation

Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA.

Macromolecule Content

Total Structure Weight: 241.69 kDa
Atom Count: 16,626
Modeled Residue Count: 2,216
Deposited Residue Count: 2,280
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Benzaldehyde lyase	A, B, C, D	570	Pseudomonas fluorescens	Mutation(s): 1 Gene Names: bznB EC: 4.1.2.38
UniProt
Find proteins for Q9F4L3 (Pseudomonas fluorescens) Explore Q9F4L3 Go to UniProtKB: Q9F4L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9F4L3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]