6M74

Crystal structure of Enterococcus hirae L-lactate oxidase M207L in complex with D-lactate form ligand

• PDB DOI: https://doi.org/10.2210/pdb6M74/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Enterococcus hirae ATCC 9790
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-03-16 Released: 2021-03-17 
• Deposition Author(s): Yoshida, H., Hiraka, K., Tsugawa, W., Sode, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.144 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 

Literature

Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper

Hiraka, K., Yoshida, H., Tsugawa, W., Asano, R., La Belle, J.T., Ikebukuro, K., Sode, K.

(2022) Protein Sci 31

• DOI: https://doi.org/10.1002/pro.4434

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.13 kDa 
• Atom Count: 3,172 
• Modelled Residue Count: 364 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate oxidase	A	368	Enterococcus hirae ATCC 9790	Mutation(s): 1  Gene Names: EHR_08130, I584_00297 EC: 1.1.3.15
UniProt
Find proteins for I6SYK8 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore I6SYK8  Go to UniProtKB:  I6SYK8

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FNR	B [auth A]	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL C17 H23 N4 O9 P YTNIXZGTHTVJBW-SCRDCRAPSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
LAC (Subject of Investigation/LOI)	C [auth A]	LACTIC ACID C3 H6 O3 JVTAAEKCZFNVCJ-UWTATZPHSA-N
PYR	D [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.144 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.13	α = 90
b = 138.13	β = 90
c = 127.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Yoshida, H., Hiraka, K., Tsugawa, W., Sode, K.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2022-10-05
  Changes: Database references, Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-11-29
  Changes: Refinement description