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- PDB-2ygw: Crystal structure of human MCD -

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Basic information

Entry
Database: PDB / ID: 2ygw
TitleCrystal structure of human MCD
ComponentsMALONYL-COA DECARBOXYLASE, MITOCHONDRIAL
KeywordsLYASE
Function / homology
Function and homology information


malonyl-CoA decarboxylase / malonyl-CoA decarboxylase activity / malonyl-CoA catabolic process / regulation of fatty acid beta-oxidation / Beta-oxidation of very long chain fatty acids / acyl-CoA metabolic process / positive regulation of fatty acid oxidation / acetyl-CoA biosynthetic process / fatty acid oxidation / peroxisomal matrix ...malonyl-CoA decarboxylase / malonyl-CoA decarboxylase activity / malonyl-CoA catabolic process / regulation of fatty acid beta-oxidation / Beta-oxidation of very long chain fatty acids / acyl-CoA metabolic process / positive regulation of fatty acid oxidation / acetyl-CoA biosynthetic process / fatty acid oxidation / peroxisomal matrix / regulation of glucose metabolic process / response to nutrient / response to ischemia / Peroxisomal protein import / fatty acid biosynthetic process / peroxisome / mitochondrial matrix / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Malonyl-CoA decarboxylase, oligemerization domain / Malonyl-CoA decarboxylase, catalytic domain / Malonyl-CoA decarboxylase, C-terminal / Malonyl-CoA decarboxylase, N-terminal / Malonyl-CoA decarboxylase, N-terminal domain superfamily / Malonyl-CoA decarboxylase / Malonyl-CoA decarboxylase, C-terminal catalytic domain superfamily / Malonyl-CoA decarboxylase C-terminal domain / Malonyl-CoA decarboxylase N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 ...Malonyl-CoA decarboxylase, oligemerization domain / Malonyl-CoA decarboxylase, catalytic domain / Malonyl-CoA decarboxylase, C-terminal / Malonyl-CoA decarboxylase, N-terminal / Malonyl-CoA decarboxylase, N-terminal domain superfamily / Malonyl-CoA decarboxylase / Malonyl-CoA decarboxylase, C-terminal catalytic domain superfamily / Malonyl-CoA decarboxylase C-terminal domain / Malonyl-CoA decarboxylase N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Aminopeptidase / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Malonyl-CoA decarboxylase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsVollmar, M. / Puranik, S. / Krojer, T. / Savitsky, P. / Allerston, C. / Yue, W.W. / Chaikuad, A. / von Delft, F. / Gileadi, O. / Kavanagh, K. ...Vollmar, M. / Puranik, S. / Krojer, T. / Savitsky, P. / Allerston, C. / Yue, W.W. / Chaikuad, A. / von Delft, F. / Gileadi, O. / Kavanagh, K. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
CitationJournal: Structure / Year: 2013
Title: Crystal Structures of Malonyl-Coenzyme a Decarboxylase Provide Insights Into its Catalytic Mechanism and Disease-Causing Mutations.
Authors: Froese, D.S. / Forouhar, F. / Tran, T.H. / Vollmar, M. / Kim, Y.S. / Lew, S. / Neely, H. / Seetharaman, J. / Shen, Y. / Xiao, R. / Acton, T.B. / Everett, J.K. / Cannone, G. / Puranik, S. / ...Authors: Froese, D.S. / Forouhar, F. / Tran, T.H. / Vollmar, M. / Kim, Y.S. / Lew, S. / Neely, H. / Seetharaman, J. / Shen, Y. / Xiao, R. / Acton, T.B. / Everett, J.K. / Cannone, G. / Puranik, S. / Savitsky, P. / Krojer, T. / Pilka, E.S. / Kiyani, W. / Lee, W.H. / Marsden, B.D. / von Delft, F. / Allerston, C.K. / Spagnolo, L. / Gileadi, O. / Montelione, G.T. / Oppermann, U. / Yue, W.W. / Tong, L.
History
DepositionApr 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL
B: MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9225
Polymers102,8602
Non-polymers623
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-17.1 kcal/mol
Surface area37440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.627, 175.342, 151.756
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 MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL /


Mass: 51429.781 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O95822, malonyl-CoA decarboxylase
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 58 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 59 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, GLU 58 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 59 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 278 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 289 TO ALA ENGINEERED RESIDUE IN CHAIN A, LYS 280 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 58 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 59 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 278 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN B, LYS 280 TO ALA
Sequence detailsN TERMINAL GTENLYFQSM SEQUENCE DUE TO CLONING AND UNCLEAVED TAG AND MUTATIONS E58A K59A E278A E279A K280A

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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: 60.99 % / Description: NONE
Crystal growDetails: 10% PEG 20000,0.1M MES (PH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→19.92 Å / Num. obs: 31699 / % possible obs: 99.7 % / Observed criterion σ(I): 1.6 / Redundancy: 5 % / Biso Wilson estimate: 94.76 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.8→29.73 Å / Cor.coef. Fo:Fc: 0.9211 / Cor.coef. Fo:Fc free: 0.8688 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=UNK. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6350. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=UNK. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=6350. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1607 5.07 %RANDOM
Rwork0.2125 ---
obs0.2146 31694 --
Displacement parametersBiso mean: 73.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.9749 Å20 Å20 Å2
2---2.6662 Å20 Å2
3---3.641 Å2
Refine analyzeLuzzati coordinate error obs: 0.453 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6249 0 6 82 6337
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016418HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.078738HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2868SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes117HARMONIC2
X-RAY DIFFRACTIONt_gen_planes979HARMONIC5
X-RAY DIFFRACTIONt_it6418HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion2.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion822SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7133SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.89 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2953 133 4.66 %
Rwork0.2562 2724 -
all0.2579 2857 -
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)
11.71870.13870.24730.7315-0.22032.5983-0.12320.1451-0.0085-0.21940.1414-0.19430.47890.0821-0.0182-0.063-0.04830.0696-0.3041-0.011-0.214147.301857.434663.673
21.24170.27440.8841.42010.05322.11290.0305-0.06710.04970.0087-0.1083-0.2140.12230.07010.0779-0.15620.04930.0124-0.2230.0615-0.176461.056366.252798.0487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID -9 - 40 AND RESID 41 - 59 AND RESID 66 - 114 AND RESID 117 - 275 AND 282 - 343 AND RESID 372 - 488)
2X-RAY DIFFRACTION2CHAIN B AND (RESID -2 - 40 AND RESID 41 - 274 AND RESID 282 - 343 AND RESID 373 - 487)

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