6S6T

Structure of Azospirillum brasilense Glutamate Synthase in a4b3 oligomeric state

PDB DOI: https://doi.org/10.2210/pdb6S6T/pdb
EM Map EMD-10105: EMDB EMDataResource

Classification: FLAVOPROTEIN
Organism(s): Azospirillum brasilense
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-03 Released: 2019-09-11
Deposition Author(s): Chaves-Sanjuan, A., Bolognesi, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM Structures of Azospirillum brasilense Glutamate Synthase in Its Oligomeric Assemblies.

Swuec, P., Chaves-Sanjuan, A., Camilloni, C., Vanoni, M.A., Bolognesi, M.

(2019) J Mol Biol 431: 4523-4526

PubMed: 31473159 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2019.08.011
Primary Citation of Related Structures:
6S6S, 6S6T, 6S6U, 6S6X

PubMed Abstract:
Bacterial NADPH-dependent glutamate synthase (GltS) is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of two L-Glu molecules from L-Gln and 2-oxo-glutarate. GltS functional unit hosts an α-subunit (αGltS) and a β-subunit (βGltS) that assemble in different αβ oligomers in solution. Here, we present the cryo-electron microscopy structures of Azospirillum brasilense GltS in four different oligomeric states (α ₄β ₃, α ₄β ₄, α ₆β ₄ and α ₆β ₆, in the 3.5- to 4.1-Å resolution range). Our study provides a comprehensive GltS model that details the inter-protomeric assemblies and allows unequivocal location of the FAD cofactor and of two electron transfer [4Fe-4S] ^+1,+2 clusters within βGltS.

Organizational Affiliation

Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.

Macromolecule Content

Total Structure Weight: 829.65 kDa
Atom Count: 56,543
Modelled Residue Count: 7,304
Deposited Residue Count: 7,506
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate synthase [NADPH] large chain	A, B, C, D	1,515	Azospirillum brasilense	Mutation(s): 0 Gene Names: gltB EC: 1.4.1.13
UniProt
Find proteins for Q05755 (Azospirillum brasilense) Explore Q05755 Go to UniProtKB: Q05755
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05755
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate synthase [NADPH] small chain	E, F, G	482	Azospirillum brasilense	Mutation(s): 0 Gene Names: gltD EC: 1.4.1.13
UniProt
Find proteins for Q05756 (Azospirillum brasilense) Explore Q05756 Go to UniProtKB: Q05756
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05756
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain X [auth G] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain X [auth G]	R [auth E], U [auth F], X [auth G]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain R [auth E] Focus chain U [auth F] Focus chain X [auth G] Interactions & Density Focus chain R [auth E] Focus chain U [auth F] Focus chain X [auth G]
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D]	H [auth A], J [auth B], L [auth C], N [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain P [auth E] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain W [auth G] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G]	P [auth E] Q [auth E] S [auth F] T [auth F] V [auth G] P [auth E], Q [auth E], S [auth F], T [auth F], V [auth G], W [auth G]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth G] Interactions & Density Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth G]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D]	I [auth A], K [auth B], M [auth C], O [auth D]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]