3GLM | pdb_00003glm

Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with crotonyl-coA

PDB DOI: https://doi.org/10.2210/pdb3GLM/pdb

Classification: LYASE
Organism(s): [Clostridium] symbiosum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-12 Released: 2009-07-28
Deposition Author(s): Kress, D., Brugel, D., Buckel, W., Essen, L.-O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.230 (Depositor), 0.185 (DCC)
R-Value Work:
0.193 (Depositor)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases

Kress, D., Brugel, D., Schall, I., Linder, D., Buckel, W., Essen, L.-O.

(2009) J Biological Chem 284: 28401-28409

PubMed: 19654317 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M109.037762
Primary Citation Related Structures:
3GF3, 3GF7, 3GLM, 3GMA

PubMed Abstract:
Glutaconyl-CoA decarboxylase (Gcd) couples the biotin-dependent decarboxylation of glutaconyl-CoA with the generation of an electrochemical Na(+) gradient. Sequencing of the genes encoding all subunits of the Clostridium symbiosum decarboxylase membrane complex revealed that it comprises two distinct biotin carrier subunits, GcdC(1) and GcdC(2), which differ in the length of a central alanine- and proline-rich linker domain. Co-crystallization of the decarboxylase subunit GcdA with the substrate glutaconyl-CoA, the product crotonyl-CoA, and the substrate analogue glutaryl-CoA, respectively, resulted in a high resolution model for substrate binding and catalysis revealing remarkable structural changes upon substrate binding. Unlike the GcdA structure from Acidaminococcus fermentans, these data suggest that in intact Gcd complexes, GcdA is associated as a tetramer crisscrossed by a network of solvent-filled tunnels.

Organizational Affiliation

Biochemie, Fachbereich Chemie, Philipps-Universität Marburg, D-35032 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 263.58 kDa
Atom Count: 18,142
Modeled Residue Count: 2,244
Deposited Residue Count: 2,352
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaconyl-CoA decarboxylase subunit A	A, B, C, D	588	[Clostridium] symbiosum	Mutation(s): 0 Gene Names: gcdA EC: 4.1.1.70
UniProt
Find proteins for B7TVP1 (Clostridium symbiosum) Explore B7TVP1 Go to UniProtKB: B7TVP1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7TVP1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COO Query on COO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	CROTONYL COENZYME A C₂₅ H₄₀ N₇ O₁₇ P₃ S KFWWCMJSYSSPSK-XBTRWLRFSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.230 (Depositor), 0.185 (DCC)
R-Value Work: 0.193 (Depositor)
R-Value Observed: 0.194 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.5	α = 90
b = 167.45	β = 89.98
c = 138.11	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-07-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-07-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-02-05
Changes: Database references
Version 1.3: 2024-03-20
Changes: Data collection, Database references, Derived calculations, Refinement description