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- PDB-3m91: Crystal structure of the prokaryotic ubiquitin-like protein (Pup)... -

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Basic information

Entry
Database: PDB / ID: 3m91
TitleCrystal structure of the prokaryotic ubiquitin-like protein (Pup) complexed with the amino terminal coiled coil of the Mycobacterium tuberculosis proteasomal ATPase Mpa
Components
  • Prokaryotic ubiquitin-like protein pup
  • Proteasome-associated ATPase
KeywordsHYDROLASE REGULATOR / coil coil alpha helix / ATP-binding / Chaperone / Nucleotide-binding / Proteasome / S-nitrosylation / Virulence / Isopeptide bond / Ubl conjugation pathway
Function / homology
Function and homology information


ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / protein pupylation / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / cell wall / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / proteasome binding ...ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / protein pupylation / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / cell wall / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / proteasome binding / protein unfolding / cellular response to nitric oxide / peptidoglycan-based cell wall / proteasomal protein catabolic process / modification-dependent protein catabolic process / protein tag activity / molecular adaptor activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Prokaryotic ubiquitin-like protein Pup / Pup-like protein / Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...Prokaryotic ubiquitin-like protein Pup / Pup-like protein / Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Prokaryotic ubiquitin-like protein Pup / Proteasome-associated ATPase / Prokaryotic ubiquitin-like protein Pup / Proteasome-associated ATPase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, T. / Li, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation.
Authors: Wang, T. / Darwin, K.H. / Li, H.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome-associated ATPase
B: Prokaryotic ubiquitin-like protein pup
C: Proteasome-associated ATPase
D: Prokaryotic ubiquitin-like protein pup


Theoretical massNumber of molelcules
Total (without water)21,6504
Polymers21,6504
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-53 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.752, 28.093, 96.233
Angle α, β, γ (deg.)90.00, 103.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 5

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA52 - 967 - 51
21GLNGLNCC52 - 967 - 51
12ALAALABB21 - 511 - 31
22ALAALADD21 - 511 - 31

NCS ensembles :
ID
1
2

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Components

#1: Protein Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / ARC / Mycobacterial proteasome ATPase


Mass: 5834.609 Da / Num. of mol.: 2 / Fragment: Coil coil domain (UNP residues:46-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Genus: mpa / Strain: H37Rv / Gene: mpa / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P63345, UniProt: P9WQN5*PLUS
#2: Protein/peptide Prokaryotic ubiquitin-like protein pup / Bacterial ubiquitin-like modifier


Mass: 4990.251 Da / Num. of mol.: 2 / Fragment: UNP residues:21-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Genus: pup / Strain: H37Rv / Gene: pup / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O33246, UniProt: P9WHN5*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 0.1M sodium acetate 16% 1,4-dioxane, 250mM sodium chloride, 2mM magnesium chloride with protease inhibitor, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 19540 / % possible obs: 88.5 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.062 / Rsym value: 0.076
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.56 / % possible all: 45

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0 / SU B: 5.719 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 992 5.1 %RANDOM
Rwork0.203 ---
obs0.204 18548 88.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0 Å2-0.62 Å2
2--3.36 Å20 Å2
3----2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 0 77 1287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0211223
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9871638
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4335148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37625.52676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03115252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8321516
X-RAY DIFFRACTIONr_chiral_restr0.1480.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02912
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5111.5755
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.04521202
X-RAY DIFFRACTIONr_scbond_it5.3293468
X-RAY DIFFRACTIONr_scangle_it9.5774.5436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A180medium positional0.060.5
2B123medium positional0.070.5
1A185loose positional0.355
2B124loose positional0.165
1A180medium thermal0.442
2B123medium thermal0.462
1A185loose thermal0.7210
2B124loose thermal0.7310
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 33 -
Rwork0.39 735 -
obs--47.58 %
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)
11.17830.198-0.48750.5524-0.87553.4607-0.06210.3306-0.2068-0.12950.10440.06340.28660.0472-0.04230.1526-0.0462-0.01760.2493-0.0790.1024-9.9671-788.96-22.9011
20.70560.25890.55552.8728-5.188711.2168-0.22430.1737-0.2114-0.03380.2292-0.2292-0.1354-0.0659-0.00490.11390.00050.0150.2257-0.05230.1613-2.4109-787.7007-8.5026
31.13070.14970.73330.64770.99994.4551-0.05960.30870.1638-0.15270.1081-0.032-0.3218-0.0058-0.04850.1579-0.05230.00540.24080.06870.1053-12.4899-782.2149-22.9323
40.64990.1861-0.66672.30283.93558.6416-0.17750.18660.2209-0.01040.22260.21190.1001-0.0548-0.04510.10440.0076-0.01940.2530.05530.1521-20.0366-783.3813-8.3666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 96
2X-RAY DIFFRACTION2B21 - 51
3X-RAY DIFFRACTION3C52 - 96
4X-RAY DIFFRACTION4D21 - 51

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