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- PDB-3u3d: Plasmodium falciparum Sir2A preferentially hydrolyzes medium and ... -

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Basic information

Entry
Database: PDB / ID: 3u3d
TitlePlasmodium falciparum Sir2A preferentially hydrolyzes medium and long chain fatty acyl lysine
Components
  • Transcriptional regulatory protein sir2 homologue
  • histone 3 myristoyl lysine 9 peptide
KeywordsHYDROLASE / Zn-binding domain / Rossmann fold domain / NAD-dependent deacylase
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / histone deacetylase activity, NAD-dependent / telomere capping / chromatin silencing complex / NAD+ binding / Chromatin modifying enzymes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / telomere organization ...Transcriptional activation of mitochondrial biogenesis / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / histone deacetylase activity, NAD-dependent / telomere capping / chromatin silencing complex / NAD+ binding / Chromatin modifying enzymes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / regulation of DNA-templated transcription / nucleolus / protein-containing complex / mitochondrion / DNA binding / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain ...Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / NAD-dependent protein deacylase Sir2A
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhou, Y. / Hao, Q.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Plasmodium falciparum Sir2A Preferentially Hydrolyzes Medium and Long Chain Fatty Acyl Lysine
Authors: Zhu, A.Y. / Zhou, Y. / Khan, S. / Deitsch, K.W. / Hao, Q. / Lin, H.
History
DepositionOct 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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: Transcriptional regulatory protein sir2 homologue
B: histone 3 myristoyl lysine 9 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8264
Polymers33,6682
Non-polymers1582
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-8 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.511, 103.328, 105.512
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Transcriptional regulatory protein sir2 homologue / Sir2A


Mass: 32050.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF13_0152, Sir2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 R2 / References: UniProt: Q8IE47, EC: 3.5.1.17
#2: Protein/peptide histone 3 myristoyl lysine 9 peptide


Mass: 1617.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.63 Å3/Da / Density % sol: 53.27 % / Mosaicity: 1.049 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 0.1M NaF, 7% Formamide, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.97 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.97 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14365 / % possible obs: 98.5 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.149 / Χ2: 2.189 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.444.40.7536890.991197.2
2.44-2.495.10.7226901.233197.5
2.49-2.535.90.8226841.302196.5
2.53-2.596.60.7057021.252199.2
2.59-2.647.10.6837041.336198.7
2.64-2.77.70.6687011.459195.9
2.7-2.778.50.6236791.35197.3
2.77-2.859.20.5457081.552198.1
2.85-2.939.40.4667021.511197.9
2.93-3.029.70.4036951.564197.3
3.02-3.139.80.3337031.544198.5
3.13-3.269.50.257371.628199.2
3.26-3.419.70.2046931.965199.7
3.41-3.589.50.177472.173199.5
3.58-3.819.40.1457082.639199.6
3.81-4.19.20.1137593.053199.7
4.1-4.528.90.0997283.733199.9
4.52-5.178.80.097493.7551100
5.17-6.518.80.0947773.5531100
6.51-507.20.0768104.105198.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JWP

3jwp


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.29 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 720 5 %RANDOM
Rwork0.2238 ---
obs0.2264 14289 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 440 Å2 / Biso mean: 59.554 Å2 / Biso min: 2.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å20 Å20 Å2
2---0.14 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 7 25 2143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0470.0222163
X-RAY DIFFRACTIONr_angle_refined_deg2.11.9692911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7815270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.38925.25678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.56415413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.804155
X-RAY DIFFRACTIONr_chiral_restr0.130.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211518
X-RAY DIFFRACTIONr_mcbond_it20.2541.51342
X-RAY DIFFRACTIONr_mcangle_it23.34622183
X-RAY DIFFRACTIONr_scbond_it52.1483821
X-RAY DIFFRACTIONr_scangle_it29.7914.5727
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 41 -
Rwork0.306 962 -
all-1003 -
obs--95.8 %
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)
1-0.0192-1.1180.13151.35951.83694.9316-0.14420.59770.03090.03880.1611-0.3658-0.17750.4968-0.01690.1822-0.03820.00350.4696-0.12440.1882-11.388-25.299-31.973
20.5892-0.2925-0.11550.57590.51241.1570.04360.08220.0101-0.0354-0.079-0.0759-0.1435-0.08180.03550.22970.0082-0.00560.12250.00320.3525-16.009-16.532-13.047
38.97156.75483.07313.23315.43724.6814-0.0512-0.0166-0.23460.3112-0.20520.11531.0299-1.58710.25640.0367-0.06810.04550.1693-0.04580.6341-27.299-32.417-20.339
4-0.12870.6144-1.9035-2.5049-0.34410.8479-0.26050.2519-0.3169-0.26220.0753-0.18770.45360.04350.18520.15680.0550.01990.306-0.21560.3722-17.908-31.168-29.699
53.1045-0.74171.90341.19550.01414.5458-0.05530.6699-0.5043-0.096-0.1547-0.2285-0.03820.35280.210.126-0.00490.0680.314-0.21080.2363-15.749-28.904-35.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 56
2X-RAY DIFFRACTION2A57 - 187
3X-RAY DIFFRACTION3A188 - 196
4X-RAY DIFFRACTION4A197 - 211
5X-RAY DIFFRACTION5A212 - 272

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