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- PDB-8ssi: Structure of Burkholderia pseudomallei deubiquitinase TssM in com... -

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Basic information

Entry
Database: PDB / ID: 8ssi
TitleStructure of Burkholderia pseudomallei deubiquitinase TssM in complex with ubiquitin
Components
  • Deubiquitinase TssM
  • Ubiquitin
KeywordsHYDROLASE / Deubiquitinase / esterase / isopeptidase
Function / homology
Function and homology information


Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Defective CFTR causes cystic fibrosis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Vif-mediated degradation of APOBEC3G
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like domain / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Polyubiquitin-C / Membrane protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSzczesna, M. / Pruneda, J.N. / Thurston, T.L.M.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142486 United States
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R011834/1 United Kingdom
Wellcome Trust209411/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: Burkholderia esterase TssM counters RNF213-mediated bacterial ubiquitylation
Authors: Szczesna, M. / Huang, Y. / Lacoursiere, R.E. / Bonini, F. / Pol, V. / Koc, F. / Ward, B. / Geurink, P.P. / Pruneda, J.N. / Thurston, T.L.M.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinase TssM
B: Ubiquitin
C: Deubiquitinase TssM
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0677
Polymers78,8614
Non-polymers2063
Water68538
1
A: Deubiquitinase TssM
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5804
Polymers39,4302
Non-polymers1492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-2 kcal/mol
Surface area15910 Å2
MethodPISA
2
C: Deubiquitinase TssM
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4873
Polymers39,4302
Non-polymers571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-1 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.517, 104.517, 193.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Deubiquitinase TssM


Mass: 30910.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: BPSS1512 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63K53
#2: Protein Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#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-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.35 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1.4 M Sodium phosphate monobasic monohydrate/Potassium phosphate dibasic pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999903 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999903 Å / Relative weight: 1
ReflectionResolution: 2.5→58.76 Å / Num. obs: 38023 / % possible obs: 100 % / Redundancy: 1.9 % / Biso Wilson estimate: 64.34 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.045 / Net I/σ(I): 8.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4205 / CC1/2: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
DIALS3.1data reduction
Aimless0.7.4data scaling
PHASERphasing
BUCCANEERmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→58.76 Å / SU ML: 0.3799 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5609
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2536 1868 4.93 %
Rwork0.227 36047 -
obs0.2283 37915 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.17 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5269 0 14 38 5321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335389
X-RAY DIFFRACTIONf_angle_d0.58987362
X-RAY DIFFRACTIONf_chiral_restr0.0427860
X-RAY DIFFRACTIONf_plane_restr0.0045976
X-RAY DIFFRACTIONf_dihedral_angle_d5.4042755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.3541450.31762717X-RAY DIFFRACTION99.58
2.57-2.640.35051410.30962697X-RAY DIFFRACTION99.82
2.64-2.730.34871350.32672716X-RAY DIFFRACTION99.79
2.73-2.830.3671410.29412750X-RAY DIFFRACTION99.9
2.83-2.940.34261290.30262735X-RAY DIFFRACTION99.97
2.94-3.070.33071510.28872736X-RAY DIFFRACTION99.9
3.07-3.230.31381190.27672763X-RAY DIFFRACTION99.9
3.23-3.440.26561510.25552756X-RAY DIFFRACTION100
3.44-3.70.29331510.24322747X-RAY DIFFRACTION100
3.7-4.080.2511560.2132776X-RAY DIFFRACTION99.97
4.08-4.660.20091380.18132805X-RAY DIFFRACTION100
4.67-5.880.22111640.19192832X-RAY DIFFRACTION100
5.88-58.760.21261470.20293017X-RAY DIFFRACTION99.94
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)
11.869508191450.236623197861-0.4231970000854.639577442471.488336213963.25243925783-0.284478392836-0.356351596955-0.1111950574550.7901419574670.2904041438250.01213758654940.8294443676780.310565267359-0.01279185266880.6829150514790.07974229447350.02888191123240.462968732995-0.03511023003280.47844016817-15.78983.13752.51
21.34650862618-0.3521161762310.05013473815761.118747734720.4561997540683.02769808563-0.0452973538639-0.2220773056530.08598626706080.1702113810220.09702895648030.2902709019240.2430865671110.0503577020359-0.06684565097640.5600992600260.0530374932998-0.06195594432370.601510074815-0.02644436756070.60097813785-23.48641.39822.086
32.97509446009-0.09039431705350.93212372112.23624892293-0.3778174038843.34657711765-0.2098884201290.2137626871780.2192589520750.06360527770190.0726140706787-0.0297448969019-0.4043646577120.3816152393210.1309618914060.46692801197-0.0794089701191-0.01670309253460.4389975489270.07130202786670.475763675263-21.31955.47-0.693
43.726027497520.3437396472340.7420440967314.371134349950.8658953168734.21896645965-0.1245820995940.7286454565020.0564156325224-1.210167243130.08441766918850.615423662266-0.648631698991-0.2243084670260.01369848010190.827453362883-0.0665346348179-0.1613892261970.6118373219260.1996271169060.638628164351-34.91261.445-22.191
51.9036420242-0.1540533864290.2563342773720.884898535380.3582954100972.960524638170.1487835036370.3341042802050.3563959227640.3279054606270.338167103740.254982312637-0.1534707510660.593510823575-0.4682363481230.642669934080.0380790120380.1111910174520.654115254358-0.1290684910980.6765831541435.69674.01611.072
62.48370624354-0.930052666799-1.347391045453.688030312960.8161431152982.62047719299-0.220960894599-0.161775064583-0.07182642169980.3647891152640.203657162744-0.158607980660.5864075861440.2148822520040.005980340397630.5831415011990.0074787142252-0.01535974307280.34459952222-0.04128396879010.446265373795-5.89370.68831.653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND ( RESID 1:75 OR RESID 101:101 ) )D1 - 75
2X-RAY DIFFRACTION1( CHAIN D AND ( RESID 1:75 OR RESID 101:101 ) )D101
3X-RAY DIFFRACTION2( CHAIN A AND RESID 207:290 )A207 - 290
4X-RAY DIFFRACTION3( CHAIN A AND RESID 291:474 )A291 - 474
5X-RAY DIFFRACTION4( CHAIN B AND ( RESID 1:75 OR RESID 101:101 ) )B1 - 75
6X-RAY DIFFRACTION4( CHAIN B AND ( RESID 1:75 OR RESID 101:101 ) )B101
7X-RAY DIFFRACTION5( CHAIN C AND RESID 207:290 )C207 - 290
8X-RAY DIFFRACTION6( CHAIN C AND RESID 291:474 )C291 - 474

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