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- PDB-1yrt: Crystal Structure analysis of the adenylyl cyclaes catalytic doma... -

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Basic information

Entry
Database: PDB / ID: 1yrt
TitleCrystal Structure analysis of the adenylyl cyclaes catalytic domain of adenylyl cyclase toxin of Bordetella pertussis in presence of c-terminal calmodulin
Components
  • Bifunctional hemolysin-adenylate cyclase
  • Calmodulin
KeywordsLAYSE / TOXIN / CyaA / CaM
Function / homology
Function and homology information


symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / : / : / : / : / : / adenylate cyclase / positive regulation of protein autophosphorylation ...symbiont-mediated cAMP intoxication of host cell / calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / : / : / : / : / : / adenylate cyclase / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / cAMP biosynthetic process / : / type 3 metabotropic glutamate receptor binding / adenylate cyclase activity / positive regulation of peptidyl-threonine phosphorylation / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / positive regulation of DNA binding / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / response to corticosterone / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / presynaptic endocytosis / regulation of synaptic vesicle exocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / adenylate cyclase binding / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / positive regulation of protein serine/threonine kinase activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / cellular response to interferon-beta / positive regulation of nitric-oxide synthase activity / presynaptic cytosol / Protein methylation / enzyme regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / sperm midpiece / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / response to amphetamine / nitric-oxide synthase regulator activity / adenylate cyclase activator activity / sarcomere / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule
Similarity search - Function
DNA polymerase; domain 1 - #920 / Alpha-Beta Plaits - #1720 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / : ...DNA polymerase; domain 1 - #920 / Alpha-Beta Plaits - #1720 / Adenylylcyclase toxin fold / Anthrax toxin, edema factor, central domain / RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / : / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / DNA polymerase; domain 1 / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bifunctional hemolysin/adenylate cyclase / Calmodulin-1 / Bifunctional hemolysin/adenylate cyclase / Calmodulin-3
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsGuo, Q. / Shen, Y. / Lee, Y.S. / Gibbs, C.S. / Mrksich, M. / Tang, W.J.
CitationJournal: Embo J. / Year: 2005
Title: Structural basis for the interaction of Bordetella pertussis adenylyl cyclase toxin with calmodulin.
Authors: Guo, Q. / Shen, Y. / Lee, Y.S. / Gibbs, C.S. / Mrksich, M. / Tang, W.J.
History
DepositionFeb 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Bifunctional hemolysin-adenylate cyclase
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0574
Polymers47,9772
Non-polymers802
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-39 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.362, 79.362, 139.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Bifunctional hemolysin-adenylate cyclase / Cyclolysin / ACT / AC-HLY


Mass: 39431.859 Da / Num. of mol.: 1 / Fragment: Calmodulin-sensitive adenylate cyclase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: cya, cyaA / Plasmid: pEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P15318, UniProt: P0DKX7*PLUS, adenylate cyclase
#2: Protein Calmodulin / CaM / CALM / CAM1


Mass: 8545.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM2, CALM3 / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pUBS520 / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: PEG4000, Isopropanol, Sodium Citrate , pH 5.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.04189,0.97948,0.97929,0.95645
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 17, 2004
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.041891
20.979481
30.979291
40.956451
ReflectionResolution: 2.1→30 Å / Num. all: 26615 / Num. obs: 25680 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.18 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 1240 random
Rwork0.22 --
all0.24 26615 -
obs0.24 25680 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3235 0 2 160 3397
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_bond_d0.023

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