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Basic information

Entry
Database: PDB / ID: 4f56
TitleThe bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5
Components
  • NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
  • peptide from Histone H3.1
KeywordsHYDROLASE / Zn-binding domain / Rossmann fold domain / NAD-dependent demalonylase and desuccinylase / mitochondrial sirtuin
Function / homology
Function and homology information


protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein deacetylation / histone deacetylase activity, NAD-dependent / negative regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species metabolic process / 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 / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / response to ischemia / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / mitochondrion organization / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / response to nutrient levels / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / mitochondrial intermembrane space / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / chromatin organization / 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 / mitochondrial inner membrane / cadherin binding / mitochondrial matrix / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / mitochondrion / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol
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 domain / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CGK / Histone H3.1 / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhou, Y. / Hao, Q.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5)
Authors: Zhou, Y. / Zhang, H. / He, B. / Du, J. / Lin, H. / Cerione, R.A. / Hao, Q.
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 15, 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 1.3Nov 8, 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_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
B: NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
C: peptide from Histone H3.1
D: peptide from Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3048
Polymers61,8224
Non-polymers1,4824
Water7,350408
1
A: NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
C: peptide from Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6524
Polymers30,9112
Non-polymers7412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-9 kcal/mol
Surface area12240 Å2
MethodPISA
2
B: NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial
D: peptide from Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6524
Polymers30,9112
Non-polymers7412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-8 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.403, 66.755, 156.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial / SIR2-like protein 5


Mass: 29674.795 Da / Num. of mol.: 2 / Fragment: UNP Residue 34-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L5, SIRT5 / Plasmid: pDEST-F1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 R2
References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide peptide from Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1236.422 Da / Num. of mol.: 2 / Fragment: UNP residue 5-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CGK / 3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid


Mass: 675.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N5O16P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.57 % / Mosaicity: 0.67 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 10000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 18, 2010
RadiationMonochromator: Horizontal bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 61730 / Num. obs: 60804 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.071 / Χ2: 2.747 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.733.30.45828301.558193.5
1.73-1.763.60.41828971.547195.7
1.76-1.794.10.37130301.634199.8
1.79-1.834.60.32930141.7161100
1.83-1.875.50.29930831.8531100
1.87-1.916.50.29230382.4011100
1.91-1.967.10.24730692.6131100
1.96-2.027.30.19330442.2691100
2.02-2.077.10.17730562.9251100
2.07-2.147.20.14430342.6321100
2.14-2.227.20.12230842.6691100
2.22-2.3170.1230693.2141100
2.31-2.417.30.09130732.9161100
2.41-2.547.30.08230712.9831100
2.54-2.77.20.07330893.0371100
2.7-2.917.20.06431283.0721100
2.91-3.27.10.05830823.199199.8
3.2-3.666.60.05230243.412196.4
3.66-4.615.70.04828583.403189.8
4.61-506.20.0532313.453196.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RIY

3riy


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2281 / WRfactor Rwork: 0.1667 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8327 / SU B: 5.48 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1705 / SU Rfree: 0.1171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 3053 5.1 %RANDOM
Rwork0.1687 ---
all0.1765 61457 --
obs0.172 60314 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.04 Å2 / Biso mean: 26.5402 Å2 / Biso min: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å20 Å2
2--0.29 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 86 408 4716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194503
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9776146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97922.591193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95215698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7371540
X-RAY DIFFRACTIONr_chiral_restr0.10.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213451
X-RAY DIFFRACTIONr_rigid_bond_restr3.03734503
X-RAY DIFFRACTIONr_sphericity_free26.8895127
X-RAY DIFFRACTIONr_sphericity_bonded11.87354658
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 187 -
Rwork0.22 3787 -
all-3974 -
obs--93.66 %

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