9EIA

A broad-substrate spectrum lactate racemase A from Isosphaera pallida in complex with copurified D-lactate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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Literature

Structural Basis for Catalysis and Substrate Specificity of a LarA Racemase with a Broad Substrate Spectrum.

Gatreddi, S.Urdiain-Arraiza, J.Desguin, B.Hausinger, R.P.Hu, J.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.11.28.625916
  • Primary Citation of Related Structures:  
    9EIA, 9EID, 9EIF

  • PubMed Abstract: 

    The LarA family consists of diverse racemases/epimerases that interconvert the diastereomers of a variety of α-hydroxyacids by using a nickel-pincer nucleotide (NPN) cofactor. The hidden redox reaction catalyzed by the NPN cofactor makes LarA enzymes attractive engineering targets for applications. However, how a LarA enzyme binds its natural substrate and recognizes different α-hydroxyacids has not been elucidated. Here, we report three high-resolution structures of the enzyme-substrate complexes of a broad-spectrum LarA enzyme from Isosphaera pallida (LarA Ip ). The substrate binding mode reveals an optimal orientation and distance between the hydride donor and acceptor, strongly supporting the proposed proton-coupled hydride transfer mechanism. The experimentally solved structures, together with the structural models of other LarA enzymes, allow us to identify the residues/structural elements critically involved in the interactions with different α-hydroxyacid substrates. Collectively, this work provides a critical structural basis for catalysis and substrate recognition of the diverse enzymes in the LarA family, thus building a foundation for enzyme engineering.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A broad-substrate spectrum lactate racemase A
A, B
425Isosphaera pallidaMutation(s): 0 
Gene Names: Isop_3476
UniProt
Find proteins for E8QWZ4 (Isosphaera pallida (strain ATCC 43644 / DSM 9630 / IS1B))
Explore E8QWZ4 
Go to UniProtKB:  E8QWZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE8QWZ4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4EY (Subject of Investigation/LOI)
Query on 4EY

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium
C12 H15 N O8 P S2
NSIYRWZYSRADIJ-GWOFURMSSA-O
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
L [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
LAC (Subject of Investigation/LOI)
Query on LAC

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
LACTIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-UWTATZPHSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)
Query on NI

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.42α = 90
b = 45.514β = 91.2
c = 119.14γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128959
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140931

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release