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- PDB-6iva: Crystal structure of the S. typhimurium oxaloacetate decarboxylas... -

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Basic information

Entry
Database: PDB / ID: 6iva
TitleCrystal structure of the S. typhimurium oxaloacetate decarboxylase beta-gamma sub-complex
Components
  • Oxaloacetate decarboxylase beta chain
  • Probable oxaloacetate decarboxylase gamma chain
KeywordsMEMBRANE PROTEIN / decarboxylase sodium pump / biotin-dependent decarboxylase
Function / homology
Function and homology information


oxaloacetate decarboxylase (Na+ extruding) / decarboxylation-driven active transmembrane transporter activity / sodium ion transmembrane transporter activity / oxaloacetate decarboxylase activity / sodium ion export across plasma membrane / sodium ion transport / lyase activity / plasma membrane
Similarity search - Function
Na+-transporting methylmalonyl-CoA/oxaloacetate decarboxylase, beta subunit / Sodium ion-translocating decarboxylase / Oxaloacetate decarboxylase, gamma chain / Na+-transporting oxaloacetate decarboxylase beta subunit / Oxaloacetate decarboxylase, gamma chain
Similarity search - Domain/homology
Oxaloacetate decarboxylase beta chain / Probable oxaloacetate decarboxylase gamma chain / Oxaloacetate decarboxylase gamma chain 2 / Oxaloacetate decarboxylase beta chain 1
Similarity search - Component
Biological speciesSalmonella enterica I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.403 Å
AuthorsXu, X. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570743 China
CitationJournal: Elife / Year: 2020
Title: Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump.
Authors: Xin Xu / Huigang Shi / Xiaowen Gong / Pu Chen / Ying Gao / Xinzheng Zhang / Song Xiang /
Abstract: The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell ...The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell membrane. It is composed of 3 subunits: the α subunit catalyzes carboxyl-transfer from oxaloacetate to biotin, the membrane integrated β subunit catalyzes the subsequent carboxyl-biotin decarboxylation and the coupled sodium transport, the γ subunit interacts with the α and β subunits and stabilizes the OAD complex. We present here structure of the OAD βγ sub-complex. The structure revealed that the β and γ subunits form a βγ hetero-hexamer with extensive interactions between the subunits and shed light on the OAD holo-enzyme assembly. Structure-guided functional studies provided insights into the sodium binding sites in the β subunit and the coupling between carboxyl-biotin decarboxylation and sodium transport by the OAD β subunit.
History
DepositionDec 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxaloacetate decarboxylase beta chain
B: Probable oxaloacetate decarboxylase gamma chain
C: Oxaloacetate decarboxylase beta chain
D: Probable oxaloacetate decarboxylase gamma chain
E: Oxaloacetate decarboxylase beta chain
F: Probable oxaloacetate decarboxylase gamma chain


Theoretical massNumber of molelcules
Total (without water)168,1976
Polymers168,1976
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18640 Å2
ΔGint-242 kcal/mol
Surface area51110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.471, 198.083, 241.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Oxaloacetate decarboxylase beta chain


Mass: 44928.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica I (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0F7JAV8, UniProt: Q8ZRY4*PLUS, oxaloacetate decarboxylase (Na+ extruding)
#2: Protein Probable oxaloacetate decarboxylase gamma chain


Mass: 11137.029 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica I (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0F7JC72, UniProt: Q03032*PLUS, oxaloacetate decarboxylase (Na+ extruding)
Sequence detailsAuthors state that this confluence may be a natural occurring mutation that happen to exist in the ...Authors state that this confluence may be a natural occurring mutation that happen to exist in the genomic DNA they used.

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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: 3.82 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium chloride, 0.1 M lithium sulfate, 0.1 M sodium citrate pH 5.5, 25% PEG1000 and 0.125% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 4.4→50 Å / Num. obs: 16715 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Net I/σ(I): 14.99
Reflection shellResolution: 4.4→4.48 Å / Mean I/σ(I) obs: 1.52 / Num. unique obs: 834 / CC1/2: 0.549

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWW

6iww


Resolution: 4.403→42.191 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 45.14
RfactorNum. reflection% reflection
Rfree0.3356 804 4.84 %
Rwork0.3096 --
obs0.3108 16615 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.403→42.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10122 0 0 0 10122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310293
X-RAY DIFFRACTIONf_angle_d0.71713977
X-RAY DIFFRACTIONf_dihedral_angle_d7.3996150
X-RAY DIFFRACTIONf_chiral_restr0.0441749
X-RAY DIFFRACTIONf_plane_restr0.0071737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4027-4.67820.39091330.40492577X-RAY DIFFRACTION98
4.6782-5.03880.36791150.36232603X-RAY DIFFRACTION99
5.0388-5.54490.43441490.37222587X-RAY DIFFRACTION100
5.5449-6.34490.36121360.37262645X-RAY DIFFRACTION100
6.3449-7.98510.3081260.31312665X-RAY DIFFRACTION100
7.9851-42.19260.30511450.25972734X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.07690.58952.3192.4935-1.69112.0294-0.22810.42680.1272-0.48870.2281-0.3364-0.24131.03680.00662.1935-0.00260.23621.63190.26661.86066.0874-38.797319.8208
22.05480.1089-2.07881.8209-1.69163.2550.75840.43540.79560.5118-0.7032-0.45810.736-0.5893-0.00583.01521.2783-0.41475.0283-0.48621.845616.8801-55.934816.3815
33.88241.14160.5075-0.14490.32725.70170.2453-0.80551.92690.18240.11090.8142-1.8105-0.50710.00032.22240.52170.02672.7103-0.15172.6174-27.1627-24.175735.0824
41.16481.4437-0.09527.65342.05033.98910.08112.41911.32521.8683-2.2061-0.73970.15611.6167-5.46042.34851.50470.10753.8381.91981.9464-17.7488-6.425632.2803
50.0047-0.3002-0.17422.2245-0.7498.07810.34120.2191-0.7719-0.1572-0.10580.28761.3978-2.13880.00012.38-0.2484-0.17122.4160.10282.2134-21.911-63.039632.8003
61.2691.03130.82743.75563.05673.16541.2859-1.35431.78450.8136-0.8757-1.1343-1.0376-0.1285-0.01012.6033-1.09330.41573.03971.32884.1801-39.5915-64.015942.6716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 13 through 432)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 43)
3X-RAY DIFFRACTION3(chain 'C' and resid 13 through 432)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 43)
5X-RAY DIFFRACTION5(chain 'E' and resid 13 through 432)
6X-RAY DIFFRACTION6(chain 'F' and resid 2 through 43)

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