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- PDB-4ae9: Structure and function of the Human Sperm-Specific Isoform of Pro... -

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Entry
Database: PDB / ID: 4ae9
TitleStructure and function of the Human Sperm-Specific Isoform of Protein Kinase A (PKA) Catalytic Subunit C alpha 2
ComponentsCAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
KeywordsTRANSFERASE
Function / homology
Function and homology information


PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly ...PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / ROBO receptors bind AKAP5 / channel activator activity / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / mitochondrial protein catabolic process / nucleotide-activated protein kinase complex / cell communication by electrical coupling involved in cardiac conduction / high-density lipoprotein particle assembly / Rap1 signalling / intracellular potassium ion homeostasis / cAMP-dependent protein kinase / regulation of protein processing / Loss of phosphorylation of MECP2 at T308 / cAMP-dependent protein kinase activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / protein localization to lipid droplet / PKA activation / cAMP-dependent protein kinase complex / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / negative regulation of interleukin-2 production / cellular response to cold / regulation of osteoblast differentiation / sperm capacitation / ciliary base / negative regulation of glycolytic process through fructose-6-phosphate / Triglyceride catabolism / protein kinase A regulatory subunit binding / mesoderm formation / cAMP/PKA signal transduction / RET signaling / Regulation of MECP2 expression and activity / sperm flagellum / Interleukin-3, Interleukin-5 and GM-CSF signaling / PKA activation in glucagon signalling / plasma membrane raft / DARPP-32 events / regulation of cardiac conduction / regulation of macroautophagy / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / postsynaptic modulation of chemical synaptic transmission / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / Hedgehog 'off' state / positive regulation of phagocytosis / Ion homeostasis / negative regulation of TORC1 signaling / regulation of proteasomal protein catabolic process / cellular response to epinephrine stimulus / sperm midpiece / calcium channel complex / Mitochondrial protein degradation / positive regulation of gluconeogenesis / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / CD209 (DC-SIGN) signaling / protein serine/threonine/tyrosine kinase activity / cellular response to glucagon stimulus / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / regulation of heart rate / protein export from nucleus / acrosomal vesicle / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / negative regulation of smoothened signaling pathway / Regulation of insulin secretion / neural tube closure / Degradation of GLI1 by the proteasome / positive regulation of cholesterol biosynthetic process / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / cytokine-mediated signaling pathway / neuromuscular junction / positive regulation of insulin secretion / VEGFA-VEGFR2 Pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / mRNA processing / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / Regulation of PLK1 Activity at G2/M Transition / GPER1 signaling / peptidyl-serine phosphorylation / manganese ion binding / Factors involved in megakaryocyte development and platelet production / cellular response to heat / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / postsynapse / protein kinase activity / regulation of cell cycle
Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHereng, T.H. / Backe, P.H. / Kahmann, J. / Scheich, C. / Bjoras, M. / Skalhegg, B.S. / Rosendal, K.R.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structure and Function of the Human Sperm-Specific Isoform of Protein Kinase a (Pka) Catalytic Subunit Calpha2
Authors: Hereng, T.H. / Backe, P.H. / Kahmann, J. / Scheich, C. / Bjoras, M. / Skalhegg, B.S. / Rosendal, K.R.
History
DepositionJan 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Jun 6, 2012Group: Other
Revision 1.3Jan 30, 2013Group: Database references / Non-polymer description
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
B: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA


Theoretical massNumber of molelcules
Total (without water)80,2372
Polymers80,2372
Non-polymers00
Water6,557364
1
A: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA


Theoretical massNumber of molelcules
Total (without water)40,1191
Polymers40,1191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA


Theoretical massNumber of molelcules
Total (without water)40,1191
Polymers40,1191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.396, 89.971, 115.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA / PKA C-ALPHA / PKA C-ALPHA 2


Mass: 40118.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: SPERMATOZOA / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA PLYSS / References: UniProt: P17612, cAMP-dependent protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN CORRESPONDS TO ISOFORM 2.

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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: 2.58 Å3/Da / Density % sol: 52.42 % / Description: NONE
Crystal growDetails: 20 % PEG 3350, 0.2 M POTASSIUM ACETATE, 5 % POLYPROPYLENE GLYCOL P400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97558
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97558 Å / Relative weight: 1
ReflectionResolution: 2.3→71.02 Å / Num. obs: 34845 / % possible obs: 97 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 2.3→7.27 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SMH

1smh


Resolution: 2.3→71.02 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.878 / SU B: 6.947 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.26431 1737 5 %RANDOM
Rwork0.1977 ---
obs0.201 32998 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.467 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→71.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 0 364 5730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225593
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.9567565
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1815664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77323.905274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64315.0591020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.711529
X-RAY DIFFRACTIONr_chiral_restr0.1180.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214217
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_it0.9521.53258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76325276
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.85932335
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5514.52279
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 129 -
Rwork0.201 2443 -
obs--97.72 %

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