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

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Basic information

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


: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / biotin carboxylase activity / acetyl-CoA carboxylase complex ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / biotin carboxylase activity / acetyl-CoA carboxylase complex / 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 / identical protein binding / metal ion 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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Rudiment single hybrid motif / 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-B37 / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)263,0776
Polymers261,6633
Non-polymers1,4153
Water18,7721042
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3854
Polymers174,4422
Non-polymers9432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12360 Å2
ΔGint-93 kcal/mol
Surface area57380 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,3854
Polymers174,4422
Non-polymers9432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-95 kcal/mol
Surface area55300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.985, 123.176, 146.157
Angle α, β, γ (deg.)90.00, 94.20, 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-B37 / 4-({4-[(2-methylquinolin-6-yl)methyl]piperidin-1-yl}carbonyl)-2-phenylquinoline / [4-(2-Methyl-quinolin-6-ylmethyl)-piperidin-1-yl]-(2-phenyl-quinolin-4-yl)-methanon


Mass: 471.592 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C32H29N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 4.24 Å3/Da / Density % sol: 70.97 %
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 315 / 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: 2.4→48.59 Å / Num. obs: 164546 / % possible obs: 96.5 % / Redundancy: 3.58 % / Biso Wilson estimate: 66.43 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.493.530.4171.9193.8
2.49-2.593.580.3552.3193.6
2.59-2.73.540.283193.9
2.7-2.853.570.2073.9194.7
2.85-3.023.560.1445.3195.6
3.02-3.263.550.17.5197
3.26-3.583.540.06610.6198.6
3.58-4.13.610.04915.1199.4
4.1-5.173.650.04117199.6
5.17-48.593.650.03419.9199.3

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.6Ldata reduction
BUSTER-TNTBUSTER 2.9.2refinement
PDB_EXTRACT3.1data extraction
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W2X

1w2x


Resolution: 2.4→43.55 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.9355 / Occupancy max: 1 / Occupancy min: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 16364 9.96 %RANDOM
Rwork0.2015 ---
obs0.2037 164285 96.4 %-
Displacement parametersBiso mean: 66.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.9764 Å20 Å20.73 Å2
2---8.5103 Å20 Å2
3---7.5339 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16507 0 108 1042 17657
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116989HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1723012HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5944SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes457HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2487HARMONIC5
X-RAY DIFFRACTIONt_it16989HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion20.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2160SEMIHARMONIC5
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_contact20385SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3194 1195 10.15 %
Rwork0.2926 10579 -
all0.2954 11774 -
obs--96.4 %
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)
10.8867-0.06770.00650.5215-0.11340.7656-0.02230.0240.1565-0.02980.0535-0.0795-0.13040.0544-0.0312-0.2982-0.0362-0.0345-0.1116-0.0095-0.129312.844416.0082-3.7675
20.7357-0.00730.03941.01-0.09491.08290.02720.02310.01840.0887-0.00960.2281-0.0271-0.2236-0.0176-0.27840.03880.0191-0.0693-0.0252-0.165444.5831-22.902437.7246
30.8864-0.0371-0.22030.9225-0.08351.07420.0106-0.0498-0.21670.1483-0.03820.04380.1904-0.08070.0276-0.21250.0005-0.0043-0.16690.0023-0.186860.0699-43.093544.6045
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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