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- PDB-3zje: A20 OTU domain in reversibly oxidised (SOH) state -

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Basic information

Entry
Database: PDB / ID: 3zje
TitleA20 OTU domain in reversibly oxidised (SOH) state
ComponentsA20P50
KeywordsHYDROLASE / UBIQUITIN / DEUBIQUITINATING ENZYME / REVERSIBLE OXIDATION / SULPHENIC ACID / CYS PROTEASE
Function / homology
Function and homology information


regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / protein K33-linked deubiquitination / protein K29-linked deubiquitination ...regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / protein K33-linked deubiquitination / protein K29-linked deubiquitination / negative regulation of B cell activation / negative regulation of chronic inflammatory response / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / negative regulation of toll-like receptor 2 signaling pathway / protein K11-linked deubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / regulation of germinal center formation / B-1 B cell homeostasis / regulation of defense response to virus by host / protein K48-linked deubiquitination / regulation of tumor necrosis factor-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / positive regulation of hepatocyte proliferation / negative regulation of bone resorption / TNFR1-induced proapoptotic signaling / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-2 production / K63-linked polyubiquitin modification-dependent protein binding / response to muramyl dipeptide / negative regulation of interleukin-6 production / positive regulation of Wnt signaling pathway / negative regulation of tumor necrosis factor production / protein deubiquitination / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / negative regulation of innate immune response / negative regulation of protein ubiquitination / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / negative regulation of smooth muscle cell proliferation / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / response to molecule of bacterial origin / kinase binding / negative regulation of inflammatory response / cellular response to hydrogen peroxide / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Ovarian tumor domain proteases / cell migration / cellular response to lipopolysaccharide / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / DNA binding / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile.
Similarity search - Domain/homology
Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKulathu, Y. / Garcia, F.J. / Mevissen, T.E.T. / Busch, M. / Arnaudo, N. / Carroll, K.S. / Barford, D. / Komander, D.
CitationJournal: Nat.Commun. / Year: 2013
Title: Regulation of A20 and Other Otu Deubiquitinases by Reversible Oxidation
Authors: Kulathu, Y. / Garcia, F.J. / Mevissen, T.E.T. / Busch, M. / Arnaudo, N. / Carroll, K.S. / Barford, D. / Komander, D.
History
DepositionJan 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: A20P50
B: A20P50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,63610
Polymers86,2992
Non-polymers3378
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-62.2 kcal/mol
Surface area29600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.850, 69.150, 84.700
Angle α, β, γ (deg.)99.14, 100.28, 97.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein A20P50 / TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3 / TNF ALPHA-INDUCED PROTEIN 3 / A20 / OTU DOMAIN- ...TUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3 / TNF ALPHA-INDUCED PROTEIN 3 / A20 / OTU DOMAIN-CONTAINING PROTEIN 7C / PUTATIVE DNA-BINDING PROTEIN A20 / ZINC FINGER PROTEIN A20


Mass: 43149.504 Da / Num. of mol.: 2 / Fragment: OTU DOMAIN, RESIDUES 1-366 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CATALYTIC CYS103 IS REVERSIBLY OXIDISED FORMING A CYS SULPHENIC ACID (SOH).
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P21580, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.85 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.2 / Details: 2-2.5 M NACL, 0.1 M MES [PH 6-6.7]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.84→34.4 Å / Num. obs: 78093 / % possible obs: 94.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 26.96 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VFJ

2vfj


Resolution: 1.84→33.717 Å / SU ML: 0.21 / σ(F): 1.97 / Phase error: 22.46 / Stereochemistry target values: ML
Details: SIDE CHAINS OF SEVERAL RESIDUES WERE NOT MODELLED DUE TO DISORDER. SOME SURFACE LOOPS ARE MISSING FROM THE STRUCTURE. CYS103 WAS REVERSIBLY OXIDISED FORMING A SULPHENIC ACID INTERMEDIATE AND ...Details: SIDE CHAINS OF SEVERAL RESIDUES WERE NOT MODELLED DUE TO DISORDER. SOME SURFACE LOOPS ARE MISSING FROM THE STRUCTURE. CYS103 WAS REVERSIBLY OXIDISED FORMING A SULPHENIC ACID INTERMEDIATE AND MODELLED AS CYS SULPHENIC ACID.
RfactorNum. reflection% reflection
Rfree0.2203 3937 5 %
Rwork0.1822 --
obs0.1841 78081 94.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→33.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 0 14 325 5641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185500
X-RAY DIFFRACTIONf_angle_d1.6787468
X-RAY DIFFRACTIONf_dihedral_angle_d16.4882038
X-RAY DIFFRACTIONf_chiral_restr0.132836
X-RAY DIFFRACTIONf_plane_restr0.008946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.86240.32591320.2792546X-RAY DIFFRACTION92
1.8624-1.8860.32951510.25342671X-RAY DIFFRACTION94
1.886-1.91080.27511370.24182671X-RAY DIFFRACTION94
1.9108-1.9370.26371260.23512622X-RAY DIFFRACTION94
1.937-1.96470.26671610.22122626X-RAY DIFFRACTION94
1.9647-1.9940.26861380.21992677X-RAY DIFFRACTION94
1.994-2.02510.25511440.20492624X-RAY DIFFRACTION95
2.0251-2.05830.23111350.18792668X-RAY DIFFRACTION94
2.0583-2.09380.22191230.19222709X-RAY DIFFRACTION94
2.0938-2.13190.20841400.18712592X-RAY DIFFRACTION94
2.1319-2.17290.23251430.18652713X-RAY DIFFRACTION95
2.1729-2.21720.24621400.18392651X-RAY DIFFRACTION95
2.2172-2.26540.21581380.18362663X-RAY DIFFRACTION95
2.2654-2.31810.25171440.1942684X-RAY DIFFRACTION95
2.3181-2.37610.22251370.18422642X-RAY DIFFRACTION94
2.3761-2.44030.20691420.18852700X-RAY DIFFRACTION95
2.4403-2.51210.24951420.18832634X-RAY DIFFRACTION95
2.5121-2.59320.25441610.18452671X-RAY DIFFRACTION95
2.5932-2.68580.19591520.18662644X-RAY DIFFRACTION95
2.6858-2.79330.24671260.18372693X-RAY DIFFRACTION95
2.7933-2.92030.21941420.19312693X-RAY DIFFRACTION95
2.9203-3.07420.21481630.18632628X-RAY DIFFRACTION95
3.0742-3.26670.20631300.18572701X-RAY DIFFRACTION95
3.2667-3.51860.20481400.16742653X-RAY DIFFRACTION95
3.5186-3.87230.18141420.15982689X-RAY DIFFRACTION95
3.8723-4.43150.19441390.14872666X-RAY DIFFRACTION95
4.4315-5.57920.1961430.15982643X-RAY DIFFRACTION94
5.5792-33.72250.24941260.2062370X-RAY DIFFRACTION85
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)
12.15730.15810.47252.6611-0.39263.4810.0824-0.1114-0.00750.3384-0.0446-0.1420.1193-0.1579-0.04230.1078-0.0381-0.00340.13310.00730.1323-18.431525.7569-12.3036
21.7047-0.10190.32822.667-0.99252.33350.03520.09610.1418-0.4793-0.1145-0.0575-0.14820.05740.03790.22360.05010.02940.1385-0.02670.1579-12.390938.337136.7136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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