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- PDB-6ytt: CO-dehydrogenase/Acetyl-CoA synthase (CODH/ACS) from Clostridium ... -

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Basic information

Entry
Database: PDB / ID: 6ytt
TitleCO-dehydrogenase/Acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum at 3.0-A resolution
Components
  • CO dehydrogenase/acetyl-CoA synthase complex, beta subunit
  • Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
KeywordsOXIDOREDUCTASE / C1-Metabolism / Carbon monoxide / metalloprotein / Acetogenic bacteria / Acetogenesis / CO-dehydrogenase/Acetyl-CoA synthase / X-ray crystal structure / Gas channeling / Waste-gas conversion.
Function / homology
Function and homology information


carbon-monoxide dehydrogenase (acceptor) / : / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / acetyl-CoA metabolic process / nickel cation binding / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 / Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Ribonuclease HI; Chain A / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Rossmann fold - #2030 / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain ...Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 / Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5 / Ribonuclease HI; Chain A / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3 / Rossmann fold - #2030 / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Helicase, Ruva Protein; domain 3 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLUORIDE ION / NICKEL (II) ION / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon-monoxide dehydrogenase (Acceptor) / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.01 Å
AuthorsWagner, T. / Lemaire, O.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)DFG-SPP 1927 WA 4053/1-1 Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum.
Authors: Lemaire, O.N. / Wagner, T.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: CO dehydrogenase/acetyl-CoA synthase complex, beta subunit
B: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
C: Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)
D: CO dehydrogenase/acetyl-CoA synthase complex, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,78243
Polymers289,9374
Non-polymers4,84439
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Core of dimeric CO-Dehydrogenase flanked by Acetyl-CoA synthase subunits
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20280 Å2
ΔGint-282 kcal/mol
Surface area95790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)298.943, 298.943, 128.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 2 types, 4 molecules ADBC

#1: Protein CO dehydrogenase/acetyl-CoA synthase complex, beta subunit


Mass: 76991.070 Da / Num. of mol.: 2 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: /
References: UniProt: U5RWA4, CO-methylating acetyl-CoA synthase
#2: Protein Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)


Mass: 67977.531 Da / Num. of mol.: 2 / Mutation: wild-type / Source method: isolated from a natural source
Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401). ...Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401).,A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401).
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: /
References: UniProt: U5RTE2, carbon-monoxide dehydrogenase (acceptor)

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Non-polymers , 7 types, 39 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: F
#7: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.56 % / Description: Brown tetragonal bi-pyramid
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: All crystallization were performed in anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96- ...Details: All crystallization were performed in anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96-well MRC 2 Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 uL of mother liquor, crystallization drop contained a mixture of 0.6 uL protein and 0.6 uL precipitant. The best diffracting crystal of CaCODH/ACS from heterotrophic growth on fructose was obtained by initial screening using the Wizard 3 & 4 screen from Jena Bioscience. The crystallization reservoir contained 100 mM BIS-TRIS propane, pH 6.5; 200 mM Sodium fluoride and 20% (w/v) Polyethylene glycol 3,350. The initial protein concentration was 16.4 mg/mL.
PH range: / / Temp details: fluctuation of 1K

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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: 1.74281 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74281 Å / Relative weight: 1
ReflectionResolution: 3.007→49.15 Å / Num. obs: 81409 / % possible obs: 96.5 % / Redundancy: 15 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.043 / Rrim(I) all: 0.168 / Net I/σ(I): 14.2
Reflection shellResolution: 3.007→3.315 Å / Redundancy: 17.5 % / Rmerge(I) obs: 1.976 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4070 / CC1/2: 0.646 / Rpim(I) all: 0.485 / Rrim(I) all: 2.035 / % possible all: 78.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.01→49.146 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 4156 5.11 %
Rwork0.1917 77245 -
obs0.1932 81401 70.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 278.84 Å2 / Biso mean: 98.4789 Å2 / Biso min: 23.55 Å2
Refinement stepCycle: final / Resolution: 3.01→49.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20215 0 174 0 20389
Biso mean--116.6 --
Num. residues----2672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.01-3.040.375260.362179852
3.04-3.080.3728100.35251681785
3.08-3.110.3809130.32312983118
3.11-3.150.3354350.360748952414
3.15-3.20.3872310.342857360416
3.2-3.240.3222360.312771975520
3.24-3.290.3273480.306388092824
3.29-3.330.2798650.2911094115931
3.33-3.390.3274920.2831399149139
3.39-3.440.3036980.28161698179647
3.44-3.50.30541060.26962131223759
3.5-3.570.30451330.24852528266169
3.57-3.630.29421700.24082892306281
3.63-3.710.28931620.24043282344490
3.71-3.790.27212070.22973549375697
3.79-3.880.25241950.22436343829100
3.88-3.970.23512070.209436073814100
3.97-4.080.20771860.18936453831100
4.08-4.20.19521730.177836823855100
4.2-4.340.20311740.168536893863100
4.34-4.490.19381900.154236313821100
4.49-4.670.19391940.148436653859100
4.67-4.880.18411960.15536773873100
4.88-5.140.17461800.162437063886100
5.14-5.460.16811880.175736803868100
5.46-5.880.22412270.191636823909100
5.88-6.470.23492070.198637033910100
6.47-7.410.23512020.237313933100
7.41-9.320.17931910.163338023993100
9.32-49.150.21452340.191639324166100
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)
13.19270.8979-0.19073.88340.39592.02230.17730.25970.4891-0.1362-0.17080.79-0.3751-0.4951-0.01470.8380.4529-0.03880.8009-0.03341.108348.77187.694823.846
25.6907-2.1431-2.345.24420.90733.0282-0.25050.2033-1.81190.4989-0.64581.3981.3524-0.39870.971.32220.02020.08461.2403-0.11991.784110.474379.863937.303
34.7266-1.3866-0.0228.92830.02062.4578-0.4728-1.11110.35091.59670.84510.53020.5057-0.2485-0.32031.09680.12350.13361.3383-0.08730.710414.1783106.984144.825
42.6249-0.87020.67043.1344-0.13183.13710.22730.1511-0.37860.1592-0.10660.03280.71380.1283-0.14560.67180.0123-0.08040.42450.08350.3645121.7403-22.34543.5145
53.51510.7959-1.19622.20531.35918.2440.7617-0.22890.21180.3186-0.21180.0462-1.2841-0.1322-0.5841.09380.1036-0.03420.7126-0.20010.914694.8056-18.5766-0.5079
61.3371-0.7713-0.05452.88370.87242.813-0.1198-0.12970.28650.37740.0611-0.3184-0.40070.31020.01940.42090.0479-0.05580.40980.05550.3593109.714439.748437.3619
75.91131.0506-2.35052.10040.45987.1618-0.31310.4154-0.3643-0.09040.05710.70120.9492-1.19910.42980.5504-0.1209-0.01140.7119-0.09070.535386.146410.496721.7406
82.6468-0.05340.40092.37420.16312.0871-0.0303-0.4327-0.05650.612-0.04320.7042-0.0857-0.8170.00670.4621-0.00540.17450.60030.00320.453789.451424.717141.6607
90.6598-0.26590.49962.0386-1.11752.09450.07290.34210.0744-0.2222-0.1603-0.04270.07160.13140.0780.22270.01940.03420.50970.03050.2944110.5220.450121.5971
101.63320.0533-0.3215.6711-0.6132.1080.0262-0.203-0.03950.9403-0.1492-0.1788-0.15520.09030.17730.36440.0003-0.00340.4552-0.00950.2792108.441620.245846.7165
114.6741-2.1016-3.51483.34860.85555.2488-0.1423-0.43460.82430.58820.2775-0.4159-0.41790.3848-0.13680.6148-0.056-0.12590.5344-0.040.4962102.741857.061347.1095
122.31710.74050.36912.9728-0.16220.52580.2363-0.6027-0.39660.4125-0.56210.0322-0.01540.20620.38520.41040.09630.05210.5392-0.03170.457387.329241.893738.2079
139.0802-0.48624.99796.02154.30758.85830.55680.59740.4510.0757-0.51140.9601-0.1538-1.5545-0.04540.62420.12570.33291.05760.11941.104660.714736.308440.264
142.6165-0.71530.1192.0761.0080.64260.17110.221-0.227-0.1944-0.02481.1132-0.0088-0.9448-0.03680.40440.12660.02220.8326-0.0690.699974.536738.893828.3474
150.7117-0.58980.50632.0930.21011.6346-0.0839-0.47330.10240.76620.19880.426-0.1843-0.4366-0.1380.69790.15060.19610.7066-0.04940.571280.019947.908752.2341
161.7985-1.26220.24541.3639-0.6951.537-0.2172-0.6022-0.13521.29110.20330.24870.1138-0.48-0.09121.11940.24120.33280.8976-0.01030.60580.390743.848265.5157
172.8485-0.49021.34742.15390.00091.6972-0.1746-0.33810.54340.5264-0.01820.4342-0.3356-0.39940.14810.74610.26060.11270.5989-0.08980.631570.537865.479240.7049
186.6224-2.16770.9012.7201-0.55011.85320.02510.6120.69520.1851-0.27730.1607-0.4384-0.04210.23610.51160.09980.01850.4369-0.04260.508283.925560.074229.7762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 311 )D1 - 311
2X-RAY DIFFRACTION2chain 'D' and (resid 312 through 473 )D312 - 473
3X-RAY DIFFRACTION3chain 'D' and (resid 474 through 708 )D474 - 708
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 320 )A1 - 320
5X-RAY DIFFRACTION5chain 'A' and (resid 321 through 708 )A321 - 708
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 105 )B3 - 105
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 136 )B106 - 136
8X-RAY DIFFRACTION8chain 'B' and (resid 137 through 217 )B137 - 217
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 523 )B218 - 523
10X-RAY DIFFRACTION10chain 'B' and (resid 524 through 631 )B524 - 631
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 73 )C2 - 73
12X-RAY DIFFRACTION12chain 'C' and (resid 74 through 106 )C74 - 106
13X-RAY DIFFRACTION13chain 'C' and (resid 107 through 136 )C107 - 136
14X-RAY DIFFRACTION14chain 'C' and (resid 137 through 182 )C137 - 182
15X-RAY DIFFRACTION15chain 'C' and (resid 183 through 351 )C183 - 351
16X-RAY DIFFRACTION16chain 'C' and (resid 352 through 400 )C352 - 400
17X-RAY DIFFRACTION17chain 'C' and (resid 401 through 523 )C401 - 523
18X-RAY DIFFRACTION18chain 'C' and (resid 524 through 631 )C524 - 631

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