6M73

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

PDB DOI: https://doi.org/10.2210/pdb6M73/pdb

Classification: OXIDOREDUCTASE
Organism(s): Enterococcus hirae ATCC 9790
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.154 (Depositor), 0.160 (DCC)
R-Value Work:
0.132 (Depositor), 0.140 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 41.15 kDa
Atom Count: 3,139
Modelled Residue Count: 364
Deposited Residue Count: 368
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate oxidase	A	368	Enterococcus hirae ATCC 9790	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6SYK8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FNR Query on FNR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
LAC (Subject of Investigation/LOI) Query on LAC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	LACTIC ACID C₃ H₆ O₃ JVTAAEKCZFNVCJ-UWTATZPHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PYR Query on PYR Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PYRUVIC ACID C₃ H₄ O₃ LCTONWCANYUPML-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.154 (Depositor), 0.160 (DCC)
R-Value Work: 0.132 (Depositor), 0.140 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.96	α = 90
b = 137.96	β = 90
c = 127.8	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Revision History (Full details and data files)

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

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Help and Resources

6M73

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)