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- PDB-1vyh: PAF-AH Holoenzyme: Lis1/Alfa2 -

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Basic information

Entry
Database: PDB / ID: 1vyh
TitlePAF-AH Holoenzyme: Lis1/Alfa2
Components
  • PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
  • PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
KeywordsHYDROLASE / LISSENCEPHALY / ACETYLHYDROLASE / PLATELET ACTIVACTING FACTOR / REGULATOR OF CYTOPLASMIC DYNEIN / CELL DIVISION / MITOSIS / NEUROGENESIS / CYTOSKELETON
Function / homology
Function and homology information


positive regulation of cellular component organization / platelet-activating factor acetyltransferase activity / corpus callosum morphogenesis / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase / maintenance of centrosome location ...positive regulation of cellular component organization / platelet-activating factor acetyltransferase activity / corpus callosum morphogenesis / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase / maintenance of centrosome location / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / radial glia-guided pyramidal neuron migration / acrosome assembly / central region of growth cone / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / cerebral cortex neuron differentiation / establishment of centrosome localization / microtubule sliding / positive regulation of cytokine-mediated signaling pathway / RHO GTPases Activate Formins / positive regulation of embryonic development / Separation of Sister Chromatids / microtubule organizing center organization / interneuron migration / layer formation in cerebral cortex / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / astral microtubule / auditory receptor cell development / nuclear membrane disassembly / Regulation of PLK1 Activity at G2/M Transition / cortical microtubule organization / positive regulation of dendritic spine morphogenesis / reelin-mediated signaling pathway / myeloid leukocyte migration / stereocilium / osteoclast development / brain morphogenesis / vesicle transport along microtubule / regulation of postsynapse organization / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / kinesin complex / Neutrophil degranulation / negative regulation of JNK cascade / microtubule associated complex / motile cilium / stem cell division / neuromuscular process controlling balance / nuclear migration / cell leading edge / dynein intermediate chain binding / dynein complex binding / transmission of nerve impulse / establishment of mitotic spindle orientation / positive regulation of macroautophagy / protein secretion / cochlea development / neuroblast proliferation / positive regulation of axon extension / lipid catabolic process / JNK cascade / axon cytoplasm / positive regulation of mitotic cell cycle / regulation of microtubule cytoskeleton organization / adult locomotory behavior / hippocampus development / phosphoprotein binding / establishment of localization in cell / brain development / cerebral cortex development / modulation of chemical synaptic transmission / kinetochore / lipid metabolic process / microtubule cytoskeleton organization / Schaffer collateral - CA1 synapse / fibrillar center / neuron migration / nuclear envelope / cell migration / negative regulation of neuron projection development / microtubule cytoskeleton / actin cytoskeleton organization / cell cortex / secretory granule lumen / spermatogenesis / nuclear membrane / microtubule binding / chemical synaptic transmission / vesicle / ficolin-1-rich granule lumen / learning or memory / protein heterodimerization activity
Similarity search - Function
LisH / : / : / PAC1 LisH domain / Dynein regulator LIS1 / LIS1, N-terminal / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / Lissencephaly type-1-like homology motif ...LisH / : / : / PAC1 LisH domain / Dynein regulator LIS1 / LIS1, N-terminal / SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / Lissencephaly type-1-like homology motif / SGNH hydrolase superfamily / LIS1 homology (LisH) motif profile. / LIS1 homology motif / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Platelet-activating factor acetylhydrolase IB subunit beta / Platelet-activating factor acetylhydrolase IB subunit alpha2 / Platelet-activating factor acetylhydrolase IB subunit alpha2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsTarricone, C. / Perrina, F. / Monzani, S. / Massimiliano, L. / Knapp, S. / Tsai, L.-H. / Derewenda, Z.S. / Musacchio, A.
CitationJournal: Neuron / Year: 2004
Title: Coupling Paf Signaling to Dynein Regulation: Structure of Lis1 in Complex with Paf-Acetylhydrolase.
Authors: Tarricone, C. / Perrina, F. / Monzani, S. / Massimiliano, L. / Kim, M.H. / Derewenda, Z.S. / Knapp, S. / Tsai, L.-H. / Musacchio, A.
History
DepositionApr 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
B: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
C: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
D: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
E: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
F: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
G: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
H: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
I: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
J: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
K: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
L: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
M: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
N: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
O: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
P: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
Q: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
R: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
S: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
T: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)723,86420
Polymers723,86420
Non-polymers00
Water00
1
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
B: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
C: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
D: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)144,7734
Polymers144,7734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
F: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
G: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
H: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)144,7734
Polymers144,7734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
I: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
J: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
K: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
L: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)144,7734
Polymers144,7734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
M: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
N: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
O: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
P: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)144,7734
Polymers144,7734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
Q: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
R: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
S: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT
T: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)144,7734
Polymers144,7734
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)205.770, 101.220, 246.130
Angle α, β, γ (deg.)90.00, 98.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT / PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / PAF ACETYLHYDROLASE 30 KDA SUBUNIT / PAF-AH 30 KDA ...PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / PAF ACETYLHYDROLASE 30 KDA SUBUNIT / PAF-AH 30 KDA SUBUNIT / PAF-AH BETA SUBUNIT / PAFAH BETA SUBUNIT


Mass: 25600.264 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q29459, UniProt: P68402*PLUS, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Protein
PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB ALPHA SUBUNIT / PAF ACETYLHYDROLASE 45 KDA SUBUNIT / PAF-AH 45 KDA SUBUNIT / PAF-AH ALPHA / PAFAH ALPHA / ...PAF ACETYLHYDROLASE 45 KDA SUBUNIT / PAF-AH 45 KDA SUBUNIT / PAF-AH ALPHA / PAFAH ALPHA / LISSENCEPHALY-1 PROTEIN / LIS-1 / PAF-AH 45 KD SUBUNIT


Mass: 46786.133 Da / Num. of mol.: 10 / Fragment: C-TERM BETA-PROPELLER, RESIDUES 1-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: BRAIN / Plasmid: PFASTBAC-HTB / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P63005
Compound detailsCATALYTIC ACTIVITY: 2-ACETYL-1-ALKYL-SN-GLYCERO-3-PHOSPHOCHOLINE + THE CATALYTIC ACTIVITY OF THE ...CATALYTIC ACTIVITY: 2-ACETYL-1-ALKYL-SN-GLYCERO-3-PHOSPHOCHOLINE + THE CATALYTIC ACTIVITY OF THE ENZYME RESIDES IN THE BETA AND GAMMA SUBUNITS, WHEREAS THE ALPHA SUBUNIT HAS REGULATORY ACTIVITY. SUBUNIT: CYTOSOLIC PAF-AH IB IS FORMED OF THREE SUBUNITS OF 45 KDA (ALPHA), 30 KDA (BETA) AND 29 KDA (GAMMA). THE CATALYTIC ACTIVITY OF THE ENZYME RESIDES IN THE BETA AND GAMMA SUBUNITS, WHEREAS THE ALPHA SUBUNIT HAS REGULATORY ACTIVITY. TRIMER FORMATION IS NOT ESSENTIAL FOR THE CATALYTIC ACTIVITY. INTERACTS WITH DYNEIN AND DYNACTIN. INTERACTS WITH RSN.

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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: 3.51 Å3/Da / Density % sol: 64.92 %
Description: 10 TRANSLATIONS WERE PERFORMED ON THE SAME CRYSTAL
Crystal growpH: 8.5 / Details: 16% PEG8K 0.2M KSCN, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 3.391→30 Å / Num. obs: 139752 / % possible obs: 96.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.096
Reflection shellResolution: 3.39→3.52 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 96.4

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXW

1fxw


Resolution: 3.4→200 Å / SU B: 31.44 / SU ML: 0.523 / Cross valid method: THROUGHOUT / ESU R Free: 0.608
RfactorNum. reflection% reflectionSelection details
Rfree0.307 5399 4 %RANDOM
Rwork0.264 ---
obs0.265 129042 96.97 %-
Displacement parametersBiso mean: 17.425 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å2-2.58 Å2
2--3.25 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 3.4→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41590 0 0 0 41590

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