7ET8

Crystal structure of thermostable AbHpaI, a class II metal dependent pyruvate aldolase, HpaI from Acinetobacter baumannii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii.

Watthaisong, P.Binlaeh, A.Jaruwat, A.Lawan, N.Tantipisit, J.Jaroensuk, J.Chuaboon, L.Phonbuppha, J.Tinikul, R.Chaiyen, P.Chitnumsub, P.Maenpuen, S.

(2021) J Biol Chem 297: 101280-101280

  • DOI: https://doi.org/10.1016/j.jbc.2021.101280
  • Primary Citation of Related Structures:  
    7ET8, 7ET9, 7ETA, 7ETB, 7ETC, 7ETD, 7ETE, 7ETF, 7ETG, 7ETH, 7ETI

  • PubMed Abstract: 

    Aldolases catalyze the reversible reactions of aldol condensation and cleavage and have strong potential for the synthesis of chiral compounds, widely used in pharmaceuticals. Here, we investigated a new Class II metal aldolase from the p-hydroxyphenylacetate degradation pathway in Acinetobacter baumannii, 4-hydroxy-2-keto-heptane-1,7-dioate aldolase (AbHpaI), which has various properties suitable for biocatalysis, including stereoselectivity/stereospecificity, broad aldehyde utilization, thermostability, and solvent tolerance. Notably, the use of Zn 2+ by AbHpaI as a native cofactor is distinct from other enzymes in this class. AbHpaI can also use other metal ion (M 2+ ) cofactors, except Ca 2+ , for catalysis. We found that Zn 2+ yielded the highest enzyme complex thermostability (T m of 87 °C) and solvent tolerance. All AbHpaI•M 2+ complexes demonstrated preferential cleavage of (4R)-2-keto-3-deoxy-D-galactonate ((4R)-KDGal) over (4S)-2-keto-3-deoxy-D-gluconate ((4S)-KDGlu), with AbHpaI•Zn 2+ displaying the highest R/S stereoselectivity ratio (sixfold higher than other M 2+ cofactors). For the aldol condensation reaction, AbHpaI•M 2+ only specifically forms (4R)-KDGal and not (4S)-KDGlu and preferentially catalyzes condensation rather than cleavage by ∼40-fold. Based on 11 X-ray structures of AbHpaI complexed with M 2+ and ligands at 1.85 to 2.0 Å resolution, the data clearly indicate that the M 2+ cofactors form an octahedral geometry with Glu151 and Asp177, pyruvate, and water molecules. Moreover, Arg72 in the Zn 2+ -bound form governs the stereoselectivity/stereospecificity of AbHpaI. X-ray structures also show that Ca 2+ binds at the trimer interface via interaction with Asp51. Hence, we conclude that AbHpaI•Zn 2+ is distinctive from its homologues in substrate stereospecificity, preference for aldol formation over cleavage, and protein robustness, and is attractive for biocatalytic applications.


  • Organizational Affiliation

    School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-2-oxoheptanedioate aldolase
A, B, C
266Acinetobacter baumanniiMutation(s): 0 
Gene Names: hpaIFD887_17235
EC: 4.1.2.52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.62α = 90
b = 90.163β = 122.33
c = 86.484γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Center for Genetic Engineering and Biotechnology (Thailand)ThailandP16-52034
Vidyasirimedhi Institute of Science and Technology (VISTEC)Thailand--

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description