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- PDB-8qwb: Crystal structure of citrate synthase from Methylophaga sulfidovorans -

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Basic information

Entry
Database: PDB / ID: 8qwb
TitleCrystal structure of citrate synthase from Methylophaga sulfidovorans
ComponentsCitrate synthase
KeywordsTRANSFERASE / Citrate Synthase
Function / homology
Function and homology information


: / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain
Similarity search - Domain/homology
Biological speciesMethylophaga sulfidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsMais, C.-N. / Bange, G. / Sendker, F.L. / Hochberg, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: bioRxiv / Year: 2024
Title: Frequent transitions in self-assembly across the evolution of a central metabolic enzyme.
Authors: Franziska L Sendker / Tabea Schlotthauer / Christopher-Nils Mais / Yat Kei Lo / Mathias Girbig / Stefan Bohn / Thomas Heimerl / Daniel Schindler / Arielle Weinstein / Brain P Metzger / ...Authors: Franziska L Sendker / Tabea Schlotthauer / Christopher-Nils Mais / Yat Kei Lo / Mathias Girbig / Stefan Bohn / Thomas Heimerl / Daniel Schindler / Arielle Weinstein / Brain P Metzger / Joseph W Thornton / Arvind Pillai / Gert Bange / Jan M Schuller / Georg K A Hochberg /
Abstract: Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are ...Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are thought to evolve because they provide some functional advantage. In many cases, however, no specific advantage is known and, in some cases, quaternary structure varies among orthologs. This has led to the proposition that self-assembly may instead vary neutrally within protein families. The extent of such variation has been difficult to ascertain because quaternary structure has until recently been difficult to measure on large scales. Here, we employ mass photometry, phylogenetics, and structural biology to interrogate the evolution of homo-oligomeric assembly across the entire phylogeny of prokaryotic citrate synthases - an enzyme with a highly conserved function. We discover a menagerie of different assembly types that come and go over the course of evolution, including cases of parallel evolution and reversions from complex to simple assemblies. Functional experiments in vitro and in vivo indicate that evolutionary transitions between different assemblies do not strongly influence enzyme catalysis. Our work suggests that enzymes can wander relatively freely through a large space of possible assemblies and demonstrates the power of characterizing structure-function relationships across entire phylogenies.
History
DepositionOct 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
D: Citrate synthase
E: Citrate synthase
F: Citrate synthase
G: Citrate synthase
H: Citrate synthase
I: Citrate synthase
J: Citrate synthase
K: Citrate synthase
L: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)537,21412
Polymers537,21412
Non-polymers00
Water00
1
A: Citrate synthase
C: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-28 kcal/mol
Surface area27580 Å2
2
B: Citrate synthase

K: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4730 Å2
ΔGint-40 kcal/mol
Surface area26690 Å2
3
D: Citrate synthase
E: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-36 kcal/mol
Surface area26270 Å2
4
F: Citrate synthase
H: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-34 kcal/mol
Surface area27060 Å2
5
G: Citrate synthase

J: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4850 Å2
ΔGint-39 kcal/mol
Surface area27170 Å2
6
I: Citrate synthase
L: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)89,5362
Polymers89,5362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-36 kcal/mol
Surface area27180 Å2
Unit cell
Length a, b, c (Å)155.690, 96.610, 203.100
Angle α, β, γ (deg.)90.00, 110.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Citrate synthase


Mass: 44767.852 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylophaga sulfidovorans (bacteria) / Gene: SAMN04488079_11738 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I4B681

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Lithium chloride, 0.1 M Citric Acid pH 5.0, 10% PEG 6000, 5mM oxaloacetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.2→48.31 Å / Num. obs: 636593 / % possible obs: 98.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.142 / Net I/σ(I): 10.29
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.2-3.292.49967550.4312.7091
3.29-3.381.71266290.5361.8611
3.38-3.471.4564650.7221.5621
3.47-3.581.03262890.8191.1111
3.58-3.70.65560900.9230.7061
3.7-3.830.53958910.9420.5821
3.83-3.970.38756780.9680.4191
3.97-4.140.2654380.9820.2831
4.14-4.320.19952920.990.2141
4.32-4.530.15850300.9930.1711
4.53-4.770.12848010.9950.1391
4.77-5.060.10845400.9950.1161
5.06-5.410.10442650.9950.1131
5.41-5.850.09739810.9960.1051
5.85-6.410.08136920.9970.0881
6.41-7.160.06333280.9980.0691
7.16-8.270.04829480.9980.0521
8.27-10.130.04125060.9990.0441
10.13-14.320.0419440.9980.0431
14.32-48.310.04310790.9980.0471

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.201→48.31 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.3245 --
Rwork0.2824 --
obs-92644 98.85 %
Refinement stepCycle: LAST / Resolution: 3.201→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30067 0 0 0 30067

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