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- PDB-1cmx: STRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDR... -

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Basic information

Entry
Database: PDB / ID: 1cmx
TitleSTRUCTURAL BASIS FOR THE SPECIFICITY OF UBIQUITIN C-TERMINAL HYDROLASES
Components(PROTEIN (UBIQUITIN YUH1-UBAL)) x 2
KeywordsHYDROLASE / UBIQUITIN HYDROLASE / UBIQUITIN / DEUBIQUITINATING ENZYME / CYSTEINE PROTEASE / ENZYME SPECIFICITY
Function / homology
Function and homology information


UCH proteinases / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / protein modification process => GO:0036211 / ubiquitin recycling / Neddylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits ...UCH proteinases / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / : / : / protein modification process => GO:0036211 / ubiquitin recycling / Neddylation / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / cytosolic ribosome / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / 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 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import
Similarity search - Function
: / Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Ribosomal L40e family / Ribosomal_L40e ...: / Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-60S ribosomal protein L40 / Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase YUH1
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJohnston, S.C. / Riddle, S.M. / Cohen, R.E. / Hill, C.P.
Citation
Journal: EMBO J. / Year: 1999
Title: Structural basis for the specificity of ubiquitin C-terminal hydrolases.
Authors: Johnston, S.C. / Riddle, S.M. / Cohen, R.E. / Hill, C.P.
#1: Journal: Embo J. / Year: 1997
Title: Crystal Structure of a Deubiquitinating Enzyme (Human Uch-L3) at 1.8 A Resolution
Authors: Johnston, S.C. / Larsen, C.N. / Cook, W.J. / Wilkinson, K.D. / Hill, C.P.
History
DepositionMay 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 27, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (UBIQUITIN YUH1-UBAL)
B: PROTEIN (UBIQUITIN YUH1-UBAL)
C: PROTEIN (UBIQUITIN YUH1-UBAL)
D: PROTEIN (UBIQUITIN YUH1-UBAL)


Theoretical massNumber of molelcules
Total (without water)69,6744
Polymers69,6744
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.300, 199.300, 36.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.996353, -0.018098, 0.08338), (0.019361, -0.999709, 0.014368), (0.083096, 0.01593, 0.996414)138.04449, 68.7913, -5.8321
2given(-0.994609, -0.018167, 0.102095), (0.019181, -0.999776, 0.00896), (0.101909, 0.01087, 0.994734)137.96919, 68.8683, -7.4825
3given(-0.995485, 0.000294, 0.094915), (0.001553, -0.999811, 0.019376), (0.094902, 0.019436, 0.995297)137.4734, 70.2087, -7.0902
4given(-0.995746, -0.011196, 0.091454), (0.012336, -0.999853, 0.011911), (0.091307, 0.012988, 0.995738)137.91611, 69.4224, -6.4478
5given(-0.995901, -0.07048, 0.056695), (0.071614, -0.997266, 0.018223), (0.055256, 0.022209, 0.998225)140.66769, 63.2826, -3.0635
6given(-0.99725, 0.003024, 0.07405), (-0.004524, -0.999788, -0.020099), (0.073974, -0.020379, 0.997052)137.4305, 70.9447, -3.7459
7given(-0.995261, -0.011771, 0.096526), (0.010528, -0.999855, -0.013377), (0.09667, -0.012298, 0.995241)137.88541, 69.7942, -6.0856
8given(-0.991403, -0.04396, 0.123242), (0.042783, -0.99901, -0.012181), (0.123655, -0.006804, 0.992302)138.11839, 67.2025, -8.7393
9given(-0.996557, -0.058399, 0.058856), (0.058071, -0.998286, -0.007268), (0.05918, -0.003825, 0.99824)139.5632, 66.1595, -3.8738
10given(-0.988787, -0.074283, 0.12955), (0.083586, -0.994183, 0.067916), (0.123751, 0.077983, 0.989244)137.6405, 62.6199, -9.9765
11given(-0.975822, 0.033297, 0.216015), (-0.021987, -0.998269, 0.054551), (0.217458, 0.048483, 0.974865)133.033, 71.1609, -16.7712
12given(-0.996871, -0.046, 0.064286), (0.047578, -0.998597, 0.023238), (0.063127, 0.026224, 0.997661)139.08749, 66.2083, -4.3703

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Components

#1: Protein PROTEIN (UBIQUITIN YUH1-UBAL)


Mass: 26276.117 Da / Num. of mol.: 2 / Fragment: ALL / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE ...Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN MM294, PLASMID P-1A2/TRPYUH1-1.
References: UniProt: P35127, EC: 3.1.2.15
#2: Protein PROTEIN (UBIQUITIN YUH1-UBAL)


Mass: 8560.831 Da / Num. of mol.: 2 / Fragment: ALL / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE ...Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN THE CYTOPLASM OF PLASMID P-1A2/TRPYUH1-1 OF SACCHAROMYCES CEREVISIAE (BAKER'S YEAST). THE EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN MM294, PLASMID P-1A2/TRPYUH1-1.
References: UniProt: P02248, UniProt: P0CG48*PLUS, EC: 3.1.2.15
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTER GLY: MODIFIED TO ALDEHYDE GLY: MODIFIED TO ALDEHYDE

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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: 2.01 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.5 / Details: 16% PEG 6000 0.1 M SODIUM ACETATE PH 4.4, pH 4.5
Crystal
*PLUS
Density % sol: 40 %
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 %PEG60001reservoir
20.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Date: Feb 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 26106 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.037 / Net I/σ(I): 14.1
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.202 / % possible all: 96.2
Reflection
*PLUS
Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.202

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR98refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1262 5 %RANDOM
Rwork0.248 ---
obs-26106 99 %-
Displacement parametersBiso mean: 55 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 0 75 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.87
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.0711.5
X-RAY DIFFRACTIONx_mcangle_it5.9292
X-RAY DIFFRACTIONx_scbond_it5.4562
X-RAY DIFFRACTIONx_scangle_it7.482.5
LS refinement shellResolution: 2.25→2.35 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.43 174
Rwork0.349 2995
Xplor fileSerial no: 1 / Param file: PARHCSDX_UBAL.PRO / Topol file: TOPHCSDX_UBAL.PRO
Software
*PLUS
Name: X-PLOR / Version: 98 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.87
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.43 / Rfactor Rwork: 0.349 / Rfactor obs: 0.349

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