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- PDB-3tvw: Crystal Structure of the humanized carboxyltransferase domain of ... -

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Basic information

Entry
Database: PDB / ID: 3tvw
TitleCrystal Structure of the humanized carboxyltransferase domain of yeast Acetyl-coA caroxylase in complex with compound 4
ComponentsAcetyl-CoA carboxylase
KeywordsLIGASE / carboxyltransferase
Function / homology
Function and homology information


Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase complex / biotin carboxylase activity ...Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase complex / biotin carboxylase activity / acetyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / long-chain fatty acid biosynthetic process / protein import into nucleus / fatty acid biosynthetic process / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal ...ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-07H / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRajamohan, F. / Marr, E. / Reyes, A. / Landro, J.A. / Anderson, M.D. / Corbett, J.W. / Dirico, K.J. / Harwood, J.H. / Tu, M. / Vajdos, F.F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure-guided Inhibitor Design for Human Acetyl-coenzyme A Carboxylase by Interspecies Active Site Conversion.
Authors: Rajamohan, F. / Marr, E. / Reyes, A.R. / Landro, J.A. / Anderson, M.D. / Corbett, J.W. / Dirico, K.J. / Harwood, J.H. / Tu, M. / Vajdos, F.F.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,8646
Polymers261,6633
Non-polymers1,2013
Water15,817878
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,2434
Polymers174,4422
Non-polymers8012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12140 Å2
ΔGint-93 kcal/mol
Surface area58180 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,2434
Polymers174,4422
Non-polymers8012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-97 kcal/mol
Surface area56770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.964, 122.858, 146.073
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acetyl-CoA carboxylase / ACC / Fatty acid synthetase 3 / mRNA transport-defective protein 7 / Biotin carboxylase


Mass: 87220.844 Da / Num. of mol.: 3 / Fragment: Carboxyltransferase domain, residues 1476-2233
Mutation: E1919Q,P1920A,H1925F,P1760S,I1762L,M1765V,Q2028E,M2030T,G2032E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ACC1, ABP2, FAS3, MTR7, YNR016C, N3175 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-07H / [4-(2H-chromen-3-ylmethyl)piperazin-1-yl]-[3-(1H-pyrazol-5-yl)phenyl]methanone


Mass: 400.473 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H24N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O

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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: 4.22 Å3/Da / Density % sol: 70.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: 100 mM NaCitrate, 12%(w/v) PEG8000, 150 mM LiSO4, 7.5% (v/v) glycerol, pH 5.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 106614 / % possible obs: 99.9 % / Biso Wilson estimate: 67.93 Å2

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.9.3refinement
PDB_EXTRACT3.1data extraction
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W2X

1w2x


Resolution: 2.8→46.96 Å / Cor.coef. Fo:Fc: 0.9387 / Cor.coef. Fo:Fc free: 0.9201 / Occupancy max: 1 / Occupancy min: 0.35 / SU R Cruickshank DPI: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 10676 10.02 %RANDOM
Rwork0.1756 ---
obs0.1786 106549 99.36 %-
Displacement parametersBiso mean: 58.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.7984 Å20 Å20.7433 Å2
2---10.4851 Å20 Å2
3---8.6867 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16554 0 90 878 17522
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117012HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1823070HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5866SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes444HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2480HARMONIC5
X-RAY DIFFRACTIONt_it17012HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion20.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2202SEMIHARMONIC5
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_contact20074SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2871 724 9.78 %
Rwork0.2256 6681 -
all0.2314 7405 -
obs--99.36 %
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)
11.1189-0.08820.070.6048-0.15960.9796-0.03790.04220.1559-0.05040.0723-0.0802-0.15150.0415-0.0344-0.2616-0.0348-0.0232-0.1623-0.0104-0.055412.730716.2246-3.4103
20.8688-0.01460.07271.1157-0.15631.19450.03280.01680.01680.07520.0060.2473-0.0101-0.2442-0.0388-0.21670.03630.0279-0.0887-0.0254-0.077944.49-23.081738.0508
30.9322-0.0166-0.22781.0971-0.03531.20660.0099-0.0807-0.2330.1744-0.02950.03710.214-0.11010.0196-0.1680.00410.0064-0.15980.0083-0.087959.9548-43.003344.5299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1480 - 2195
2X-RAY DIFFRACTION2{ B|* }B1480 - 2189
3X-RAY DIFFRACTION3{ C|* }C1492 - 2192

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