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- PDB-1um2: Crystal Structure of the Vma1-Derived Endonuclease with the Ligat... -

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Basic information

Entry
Database: PDB / ID: 1um2
TitleCrystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment
Components
  • 21-mer from Vacuolar ATP synthase catalytic subunit A
  • ENDONUCLEASE PI-SCEI
KeywordsHYDROLASE / Protein splicing / Vma1-derived endonuclease / VDE / intein / extein / thiazolidine
Function / homology
Function and homology information


Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / intron homing / protein metabolic process / intein-mediated protein splicing / fungal-type vacuole membrane / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / Golgi membrane / mRNA binding / DNA binding / ATP binding
Similarity search - Function
Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease ...Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Beta Complex / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
V-type proton ATPase catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMizutani, R. / Anraku, Y. / Satow, Y.
Citation
Journal: J.Synchrotron Radiat. / Year: 2004
Title: Protein splicing of yeast VMA1-derived endonuclease via thiazolidine intermediates.
Authors: Mizutani, R. / Anraku, Y. / Satow, Y.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides
Authors: Mizutani, R. / Nogami, S. / Kawasaki, M. / Ohya, Y. / Anraku, Y. / Satow, Y.
History
DepositionSep 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.5Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDONUCLEASE PI-SCEI
B: ENDONUCLEASE PI-SCEI
C: 21-mer from Vacuolar ATP synthase catalytic subunit A
D: 21-mer from Vacuolar ATP synthase catalytic subunit A


Theoretical massNumber of molelcules
Total (without water)106,3904
Polymers106,3904
Non-polymers00
Water2,756153
1
A: ENDONUCLEASE PI-SCEI
C: 21-mer from Vacuolar ATP synthase catalytic subunit A


Theoretical massNumber of molelcules
Total (without water)53,1952
Polymers53,1952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDONUCLEASE PI-SCEI
D: 21-mer from Vacuolar ATP synthase catalytic subunit A


Theoretical massNumber of molelcules
Total (without water)53,1952
Polymers53,1952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.4, 70.4, 58.0
Angle α, β, γ (deg.)100.4, 98.7, 78.9
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ENDONUCLEASE PI-SCEI / VMA1-DERIVED ENDONUCLEASE X10SNS


Mass: 50963.789 Da / Num. of mol.: 2 / Mutation: C284S, H362N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: vma1 / Plasmid: pET-17b-VDE-X10SNS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17255, H+-transporting two-sector ATPase
#2: Protein/peptide 21-mer from Vacuolar ATP synthase catalytic subunit A / 21-mer from VMA1-DERIVED ENDONUCLEASE X10SNS


Mass: 2231.400 Da / Num. of mol.: 2 / Mutation: C738S
Source method: isolated from a genetically manipulated source
Details: The N-extein segments: residues 273-283 and C-extein segments: 738-747 were ligated by protein splicing. residue 283 links with residue 738
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: vma1 / Plasmid: pET-17b-VDE-X10SNS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17255, H+-transporting two-sector ATPase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, BistrisHCl, 2-mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.7 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 17, 2000
Details: DOUBLE CRYSTAL MONOCHROMATOR AND BENT-CYLINDER MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 20700 / Num. obs: 20700 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.141 / Num. unique all: 1519 / % possible all: 60.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1jva

1jva


Resolution: 2.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.283 922 RANDOM
Rwork0.214 --
all0.217 20700 -
obs0.217 20700 -
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 0 153 6865
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.01

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