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- PDB-3tz3: Crystal Structure of the humanized carboxyltransferase domain of ... -

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Basic information

Entry
Database: PDB / ID: 3tz3
TitleCrystal Structure of the humanized carboxyltransferase domain of yeast Acetyl-coA caroxylase in complex with compound 2
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 / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process ...Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / acetyl-CoA biosynthetic process / 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, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-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, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-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 / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 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-B36 / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 26, 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)262,9966
Polymers261,6633
Non-polymers1,3343
Water15,457858
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3314
Polymers174,4422
Non-polymers8892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12830 Å2
ΔGint-90 kcal/mol
Surface area56520 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3314
Polymers174,4422
Non-polymers8892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-93 kcal/mol
Surface area54830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.850, 123.370, 145.100
Angle α, β, γ (deg.)90.000, 94.410, 90.000
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, UNP 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-B36 / 6-{[1-(anthracen-9-ylcarbonyl)piperidin-4-yl]methyl}-2-methylquinoline / Anthracen-9-yl-[4-(2-methyl-quinolin-6-ylmethyl)-piperidin-1-yl]-methanon


Mass: 444.567 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H28N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 858 / 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: 4.21 Å3/Da / Density % sol: 70.78 %
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: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→44.75 Å / Num. all: 110128 / Num. obs: 110128 / % possible obs: 100 % / Biso Wilson estimate: 82.77 Å2

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.1data extraction
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB_ENTRY 1W2X

1w2x


Resolution: 2.7→44.75 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9191 / Occupancy max: 1 / Occupancy min: 0.65 / SU R Cruickshank DPI: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 10911 9.91 %RANDOM
Rwork0.2061 ---
obs0.2093 110128 92.44 %-
Displacement parametersBiso max: 218 Å2 / Biso mean: 72.869 Å2 / Biso min: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1-5.188 Å20 Å2-0.5562 Å2
2---3.9428 Å20 Å2
3----1.2452 Å2
Refine analyzeLuzzati coordinate error obs: 0.421 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16444 0 102 858 17404
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5918SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes456HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2470HARMONIC5
X-RAY DIFFRACTIONt_it16913HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2149SEMIHARMONIC5
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_contact20313SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16913HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg22912HARMONIC21.18
X-RAY DIFFRACTIONt_omega_torsion3.09
X-RAY DIFFRACTIONt_other_torsion20.75
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2641 743 9.26 %
Rwork0.2304 7281 -
all0.2336 8024 -
obs--92.44 %
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)
10.97340.0260.11250.56650.12041.0075-0.0353-0.03530.15770.04410.03930.0732-0.1461-0.0662-0.004-0.33520.0349-0.0381-0.10570.0198-0.3794-12.846334.10683.7495
20.81850.03610.02941.01290.03061.19030.0253-0.03390.0218-0.0369-0.0244-0.2025-0.05440.2629-0.0009-0.3562-0.01250.0012-0.11570.023-0.4776-44.6098-4.7374-37.5116
30.94030.056-0.27310.96560.00181.4911-0.00620.0736-0.2012-0.1614-0.0134-0.01760.22740.05240.0196-0.26540.0041-0.0238-0.2245-0.0141-0.4801-60.0638-25.2262-45.3307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1480 - 2193
2X-RAY DIFFRACTION2{ B|* }B1480 - 2191
3X-RAY DIFFRACTION3{ C|* }C1494 - 2191

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