9HDE | pdb_00009hde

Crystal structure of methionine gamma-lyase (K209Q variant) from Brevibacterium aurantiacum in complex with PLP and alpha-ketobutyrate

PDB DOI: https://doi.org/10.2210/pdb9HDE/pdb

Classification: LYASE
Organism(s): Brevibacterium aurantiacum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-12 Released: 2025-10-22
Deposition Author(s): Kopecny, D., Ferchaud, N., Briozzo, P.
Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, Other government, Agence Nationale de la Recherche (ANR), Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.265 (Depositor), 0.256 (DCC)
R-Value Work:
0.258 (Depositor), 0.247 (DCC)
R-Value Observed:
0.258 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Functional and structural characterization of methionine gamma-lyases from Brevibacterium bacteria: insights into cofactor retention

Ferchaud, N., Boyer, A., Odegard, B., Hentati, S., Simonson, T., Machover, D., Kopecny, D., Briozzo, P.

To be published.

Macromolecule Content

Total Structure Weight: 1,037.78 kDa
Atom Count: 68,557
Modeled Residue Count: 9,292
Deposited Residue Count: 9,912
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystathionine gamma-synthase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	413	Brevibacterium aurantiacum	Mutation(s): 1 Gene Names: BAUR9175_03070, BAUR920_03040, BAURA63_02933, BAURA86_00394 EC: 4.4.1.11 (PDB Primary Data), 4.4.1.2 (UniProt)
UniProt
Find proteins for A0A2H1K3G9 (Brevibacterium aurantiacum) Explore A0A2H1K3G9 Go to UniProtKB: A0A2H1K3G9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2H1K3G9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4LM (Subject of Investigation/LOI) Query on 4LM Download Ideal Coordinates CCD File SDF format, chain BB [auth N] SDF format, chain CA [auth A] SDF format, chain DA [auth B] SDF format, chain FB [auth O] SDF format, chain GB [auth P] SDF format, chain IB [auth Q] SDF format, chain JA [auth C] SDF format, chain JB [auth R] SDF format, chain KA [auth D] SDF format, chain KB [auth S] SDF format, chain LB [auth T] SDF format, chain MA [auth E] SDF format, chain MB [auth U] SDF format, chain NA [auth F] SDF format, chain NB [auth V] SDF format, chain PA [auth G] SDF format, chain PB [auth W] SDF format, chain QA [auth H] SDF format, chain RB [auth X] SDF format, chain TA [auth I] SDF format, chain UA [auth J] SDF format, chain WA [auth K] SDF format, chain XA [auth L] SDF format, chain ZA [auth M] MOL2 format, chain BB [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain FB [auth O] MOL2 format, chain GB [auth P] MOL2 format, chain IB [auth Q] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth R] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth S] MOL2 format, chain LB [auth T] MOL2 format, chain MA [auth E] MOL2 format, chain MB [auth U] MOL2 format, chain NA [auth F] MOL2 format, chain NB [auth V] MOL2 format, chain PA [auth G] MOL2 format, chain PB [auth W] MOL2 format, chain QA [auth H] MOL2 format, chain RB [auth X] MOL2 format, chain TA [auth I] MOL2 format, chain UA [auth J] MOL2 format, chain WA [auth K] MOL2 format, chain XA [auth L] MOL2 format, chain ZA [auth M] mmCIF format, chain BB [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain FB [auth O] mmCIF format, chain GB [auth P] mmCIF format, chain IB [auth Q] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth R] mmCIF format, chain KA [auth D] mmCIF format, chain KB [auth S] mmCIF format, chain LB [auth T] mmCIF format, chain MA [auth E] mmCIF format, chain MB [auth U] mmCIF format, chain NA [auth F] mmCIF format, chain NB [auth V] mmCIF format, chain PA [auth G] mmCIF format, chain PB [auth W] mmCIF format, chain QA [auth H] mmCIF format, chain RB [auth X] mmCIF format, chain TA [auth I] mmCIF format, chain UA [auth J] mmCIF format, chain WA [auth K] mmCIF format, chain XA [auth L] mmCIF format, chain ZA [auth M]	BB [auth N] CA [auth A] DA [auth B] FB [auth O] GB [auth P] BB [auth N], CA [auth A], DA [auth B], FB [auth O], GB [auth P], IB [auth Q], JA [auth C], JB [auth R], KA [auth D], KB [auth S], LB [auth T], MA [auth E], MB [auth U], NA [auth F], NB [auth V], PA [auth G], PB [auth W], QA [auth H], RB [auth X], TA [auth I], UA [auth J], WA [auth K], XA [auth L], ZA [auth M]	(2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid C₁₂ H₁₅ N₂ O₇ P BBYSOXSBJOWRNU-VMTXVVAMSA-N		Interactions Focus chain BB [auth N] Focus chain CA [auth A] Focus chain DA [auth B] Focus chain FB [auth O] Focus chain GB [auth P] Focus chain IB [auth Q] Focus chain JA [auth C] Focus chain JB [auth R] Focus chain KA [auth D] Focus chain KB [auth S] Focus chain LB [auth T] Focus chain MA [auth E] Focus chain MB [auth U] Focus chain NA [auth F] Focus chain NB [auth V] Focus chain PA [auth G] Focus chain PB [auth W] Focus chain QA [auth H] Focus chain RB [auth X] Focus chain TA [auth I] Focus chain UA [auth J] Focus chain WA [auth K] Focus chain XA [auth L] Focus chain ZA [auth M] Interactions & Density Focus chain BB [auth N] Focus chain CA [auth A] Focus chain DA [auth B] Focus chain FB [auth O] Focus chain GB [auth P] Focus chain IB [auth Q] Focus chain JA [auth C] Focus chain JB [auth R] Focus chain KA [auth D] Focus chain KB [auth S] Focus chain LB [auth T] Focus chain MA [auth E] Focus chain MB [auth U] Focus chain NA [auth F] Focus chain NB [auth V] Focus chain PA [auth G] Focus chain PB [auth W] Focus chain QA [auth H] Focus chain RB [auth X] Focus chain TA [auth I] Focus chain UA [auth J] Focus chain WA [auth K] Focus chain XA [auth L] Focus chain ZA [auth M]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain DB [auth N] SDF format, chain EA [auth B] SDF format, chain HA [auth B] SDF format, chain QB [auth X] SDF format, chain RA [auth H] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain DB [auth N] MOL2 format, chain EA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain QB [auth X] MOL2 format, chain RA [auth H] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain DB [auth N] mmCIF format, chain EA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain QB [auth X] mmCIF format, chain RA [auth H] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	DB [auth N] EA [auth B] HA [auth B] QB [auth X] RA [auth H] DB [auth N], EA [auth B], HA [auth B], QB [auth X], RA [auth H], Y [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DB [auth N] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain QB [auth X] Focus chain RA [auth H] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain DB [auth N] Focus chain EA [auth B] Focus chain HA [auth B] Focus chain QB [auth X] Focus chain RA [auth H] Focus chain Y [auth A] Focus chain Z [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth M] SDF format, chain BA [auth A] SDF format, chain CB [auth N] SDF format, chain EB [auth O] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HB [auth P] SDF format, chain IA [auth C] SDF format, chain LA [auth D] SDF format, chain OA [auth F] SDF format, chain OB [auth V] SDF format, chain SA [auth H] SDF format, chain VA [auth J] SDF format, chain YA [auth L] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth M] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth N] MOL2 format, chain EB [auth O] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HB [auth P] MOL2 format, chain IA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain OA [auth F] MOL2 format, chain OB [auth V] MOL2 format, chain SA [auth H] MOL2 format, chain VA [auth J] MOL2 format, chain YA [auth L] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth M] mmCIF format, chain BA [auth A] mmCIF format, chain CB [auth N] mmCIF format, chain EB [auth O] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HB [auth P] mmCIF format, chain IA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain OA [auth F] mmCIF format, chain OB [auth V] mmCIF format, chain SA [auth H] mmCIF format, chain VA [auth J] mmCIF format, chain YA [auth L]	AA [auth A] AB [auth M] BA [auth A] CB [auth N] EB [auth O] AA [auth A], AB [auth M], BA [auth A], CB [auth N], EB [auth O], FA [auth B], GA [auth B], HB [auth P], IA [auth C], LA [auth D], OA [auth F], OB [auth V], SA [auth H], VA [auth J], YA [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain AB [auth M] Focus chain BA [auth A] Focus chain CB [auth N] Focus chain EB [auth O] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HB [auth P] Focus chain IA [auth C] Focus chain LA [auth D] Focus chain OA [auth F] Focus chain OB [auth V] Focus chain SA [auth H] Focus chain VA [auth J] Focus chain YA [auth L] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth M] Focus chain BA [auth A] Focus chain CB [auth N] Focus chain EB [auth O] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HB [auth P] Focus chain IA [auth C] Focus chain LA [auth D] Focus chain OA [auth F] Focus chain OB [auth V] Focus chain SA [auth H] Focus chain VA [auth J] Focus chain YA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.265 (Depositor), 0.256 (DCC)
R-Value Work: 0.258 (Depositor), 0.247 (DCC)
R-Value Observed: 0.258 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.328	α = 90
b = 155.89	β = 90.24
c = 232.079	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
Coot	model building
BUSTER	refinement
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Kopecny, D.

Ferchaud, N.

Briozzo, P.

Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	MOBILITY 8J23FR011
Other government		FR 49271QH PHC BARRANDE
Agence Nationale de la Recherche (ANR)	France	France 2023 ANR-11-IDEX-0003, Jean d'Alembert fellowship at Paris-Saclay
Other private		IMEBATRACA