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- PDB-5vj1: Crystal structure of a Pseudomonas malonate decarboxylase hetero-... -

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Basic information

Entry
Database: PDB / ID: 5vj1
TitleCrystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with coenzyme A
Components
  • MdcA
  • MdcC
  • MdcD
  • MdcE
KeywordsTRANSFERASE / acetyl-CoA carboxylase / coa transferase / acp transferase
Function / homology
Function and homology information


malonyl-S-ACP:biotin-protein carboxyltransferase / biotin-independent malonate decarboxylase / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / carboxy-lyase activity / acyl carrier activity / fatty acid biosynthetic process / transferase activity / carbohydrate metabolic process / cytoplasm
Similarity search - Function
Malonate decarboxylase delta subunit / Malonate decarboxylase/citrate lyase acyl carrier protein / Malonate decarboxylase delta subunit (MdcD) / Acetyl-S-ACP:malonate ACP transferase / Biotin-dependent malonate decarboxylase, gamma subunit / Biotin-independent malonate decarboxylase, beta subunit / Malonate decarboxylase gamma subunit / Malonate decarboxylase, alpha subunit, transporter / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. ...Malonate decarboxylase delta subunit / Malonate decarboxylase/citrate lyase acyl carrier protein / Malonate decarboxylase delta subunit (MdcD) / Acetyl-S-ACP:malonate ACP transferase / Biotin-dependent malonate decarboxylase, gamma subunit / Biotin-independent malonate decarboxylase, beta subunit / Malonate decarboxylase gamma subunit / Malonate decarboxylase, alpha subunit, transporter / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / NagB/RpiA transferase-like / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Biotin-independent malonate decarboxylase subunit beta / Malonyl-S-ACP:biotin-protein carboxyltransferase MADD / Malonate decarboxylase acyl carrier protein / Malonate decarboxylase gamma subunit / Malonate decarboxylase beta subunit / Malonate decarboxylase alpha subunit
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Pseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å
AuthorsMaderbocus, R. / Tong, L.
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer.
Authors: Maderbocus, R. / Fields, B.L. / Hamilton, K. / Luo, S. / Tran, T.H. / Dietrich, L.E.P. / Tong, L.
History
DepositionApr 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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

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Assembly

Deposited unit
A: MdcA
C: MdcC
D: MdcD
E: MdcE
I: MdcA
K: MdcC
L: MdcD
M: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,40511
Polymers265,8348
Non-polymers1,5713
Water00
1
A: MdcA
C: MdcC
D: MdcD
E: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7206
Polymers132,9174
Non-polymers8032
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: MdcA
K: MdcC
L: MdcD
M: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,6855
Polymers132,9174
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: MdcA
C: MdcC
I: MdcA
K: MdcC
hetero molecules

L: MdcD
M: MdcE
hetero molecules

D: MdcD
E: MdcE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,40511
Polymers265,8348
Non-polymers1,5713
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area34210 Å2
ΔGint-166 kcal/mol
Surface area75190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.740, 163.560, 100.440
Angle α, β, γ (deg.)90.00, 94.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules AICKDLEM

#1: Protein MdcA / Malonate decarboxylase alpha subunit


Mass: 61501.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: mdcA, PA0208 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6T0
#2: Protein MdcC / Malonate decarboxylase acyl carrier protein / Malonate decarboxylase subunit delta


Mass: 10692.981 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria)
Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: mdcC, PFL_5818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K4F7
#3: Protein MdcD / Biotin-independent malonate decarboxylase subunit beta / Malonate decarboxylase subunit beta / ...Biotin-independent malonate decarboxylase subunit beta / Malonate decarboxylase subunit beta / Malonyl-S-ACP:biotin-protein carboxyltransferase MADC / Methylmalonyl-CoA carboxyltransferase 12S subunit


Mass: 30371.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: madC, mdcD, AO964_31600, AOY09_06294, BH593_13640, PAERUG_E15_London_28_01_14_07061, PAERUG_P32_London_17_VIM_2_10_11_04127, PAMH19_0209
Production host: Escherichia coli (E. coli)
References: UniProt: A0A071KS24, UniProt: Q9I6S7*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase, methylmalonyl-CoA carboxytransferase
#4: Protein MdcE / Biotin-independent malonate decarboxylase subunit gamma / Malonate decarboxylase / gamma subunit / ...Biotin-independent malonate decarboxylase subunit gamma / Malonate decarboxylase / gamma subunit / Malonyl-S-ACP:biotin-protein carboxyltransferase MADD


Mass: 30351.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: madD, AO964_31595, AOY09_06293, PAERUG_E15_London_28_01_14_07062, PAERUG_P32_London_17_VIM_2_10_11_04128
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0C6EV56, UniProt: Q9I6S6*PLUS, malonyl-S-ACP:biotin-protein carboxyltransferase

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) PEG3350 and 8% Tacsimate / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2016 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 63210 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12
Reflection shellResolution: 3→3.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 1.7 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.995→47.901 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 3188 5.05 %
Rwork0.1731 --
obs0.1762 63159 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.995→47.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18104 0 97 0 18201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118568
X-RAY DIFFRACTIONf_angle_d1.51125224
X-RAY DIFFRACTIONf_dihedral_angle_d15.9366928
X-RAY DIFFRACTIONf_chiral_restr0.0562786
X-RAY DIFFRACTIONf_plane_restr0.0083364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9949-3.03960.39021150.32922459X-RAY DIFFRACTION93
3.0396-3.08710.35331280.29742656X-RAY DIFFRACTION100
3.0871-3.13770.37361350.28132580X-RAY DIFFRACTION99
3.1377-3.19180.35321170.28132614X-RAY DIFFRACTION99
3.1918-3.24980.31691600.26032612X-RAY DIFFRACTION99
3.2498-3.31230.31921160.25062646X-RAY DIFFRACTION99
3.3123-3.37990.29081270.24942584X-RAY DIFFRACTION99
3.3799-3.45340.28321330.24582600X-RAY DIFFRACTION99
3.4534-3.53370.29011500.23852574X-RAY DIFFRACTION98
3.5337-3.6220.3151320.21472583X-RAY DIFFRACTION99
3.622-3.71990.26851360.20452637X-RAY DIFFRACTION99
3.7199-3.82930.24521290.17232618X-RAY DIFFRACTION100
3.8293-3.95290.23991630.16732600X-RAY DIFFRACTION100
3.9529-4.09410.21451580.15672610X-RAY DIFFRACTION99
4.0941-4.25790.22271590.1442599X-RAY DIFFRACTION99
4.2579-4.45160.16851490.13782587X-RAY DIFFRACTION99
4.4516-4.68610.19331490.13252610X-RAY DIFFRACTION99
4.6861-4.97940.22091340.132636X-RAY DIFFRACTION100
4.9794-5.36340.20461350.14142637X-RAY DIFFRACTION100
5.3634-5.90220.21081410.15232643X-RAY DIFFRACTION99
5.9022-6.75430.24531540.15692593X-RAY DIFFRACTION98
6.7543-8.50190.18211160.13412666X-RAY DIFFRACTION99
8.5019-47.90660.17381520.13572627X-RAY DIFFRACTION98

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