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- PDB-5x3f: Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain -

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Basic information

Entry
Database: PDB / ID: 5x3f
TitleCrystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain
Components
  • Putrescine aminotransferase,Immunoglobulin G-binding protein A
  • Zpa963,cAMP-dependent protein kinase catalytic subunit alpha
KeywordsTRANSFERASE / synthetic protein / LYASE
Function / homology
Function and homology information


diamine transaminase / putrescine-2-oxoglutarate transaminase / diamine transaminase activity / putrescine--2-oxoglutarate transaminase activity / L-lysine catabolic process / putrescine catabolic process / spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase ...diamine transaminase / putrescine-2-oxoglutarate transaminase / diamine transaminase activity / putrescine--2-oxoglutarate transaminase activity / L-lysine catabolic process / putrescine catabolic process / spontaneous exocytosis of neurotransmitter / HDL assembly / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / MAPK6/MAPK4 signaling / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / CD209 (DC-SIGN) signaling / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / RET signaling / Ion homeostasis / VEGFA-VEGFR2 Pathway / nucleotide-activated protein kinase complex / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / IgG binding / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / mesoderm formation / sperm flagellum / regulation of proteasomal protein catabolic process / negative regulation of smoothened signaling pathway / protein kinase A signaling / positive regulation of gluconeogenesis / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / neural tube closure / cellular response to glucose stimulus / modulation of chemical synaptic transmission / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / mRNA processing / small GTPase binding / pyridoxal phosphate binding / presynapse / cellular response to heat / manganese ion binding / postsynapse / peptidyl-serine phosphorylation / dendritic spine / regulation of cell cycle / protein kinase activity / nuclear speck / protein domain specific binding / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein homodimerization activity / protein-containing complex
Similarity search - Function
Putrescine aminotransferase / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / : / LysM domain / LysM domain profile. ...Putrescine aminotransferase / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / : / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / Aminotransferases class-III pyridoxal-phosphate attachment site. / YSIRK type signal peptide / Aminotransferase class-III / Aminotransferase class-III / cAMP-dependent protein kinase catalytic subunit / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / Immunoglobulin G-binding protein A / Putrescine aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Staphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsYoun, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.
CitationJournal: Sci Rep / Year: 2017
Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.
History
DepositionFeb 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putrescine aminotransferase,Immunoglobulin G-binding protein A
B: Zpa963,cAMP-dependent protein kinase catalytic subunit alpha


Theoretical massNumber of molelcules
Total (without water)99,9312
Polymers99,9312
Non-polymers00
Water0
1
A: Putrescine aminotransferase,Immunoglobulin G-binding protein A
B: Zpa963,cAMP-dependent protein kinase catalytic subunit alpha

A: Putrescine aminotransferase,Immunoglobulin G-binding protein A
B: Zpa963,cAMP-dependent protein kinase catalytic subunit alpha

A: Putrescine aminotransferase,Immunoglobulin G-binding protein A
B: Zpa963,cAMP-dependent protein kinase catalytic subunit alpha

A: Putrescine aminotransferase,Immunoglobulin G-binding protein A
B: Zpa963,cAMP-dependent protein kinase catalytic subunit alpha


Theoretical massNumber of molelcules
Total (without water)399,7258
Polymers399,7258
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Unit cell
Length a, b, c (Å)140.518, 153.496, 205.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Putrescine aminotransferase,Immunoglobulin G-binding protein A / Putrescine--2-oxoglutaric acid transaminase / PATase / IgG-binding protein A / Staphylococcal protein A


Mass: 54451.414 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 7-453,220-269 / Mutation: N222V, G240A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Putrescine aminotransferase (UNP RESIDUES 7-453) and Immunoglobulin G-binding protein A (UNP RESIDUES 220-269)
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Staphylococcus aureus (bacteria)
Strain: K12 / Gene: patA, ygjG, b3073, JW5510, spa / Production host: Escherichia coli (E. coli)
References: UniProt: P42588, UniProt: P38507, putrescine-2-oxoglutarate transaminase
#2: Protein Zpa963,cAMP-dependent protein kinase catalytic subunit alpha / PKA C-alpha


Mass: 45479.789 Da / Num. of mol.: 1 / Fragment: residues 97-156,UNP RESIDUES 11-343
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Zpa963 and cAMP-dependent protein kinase catalytic subunit alpha (UNP RESIDUES 11-343)
Source: (gene. exp.) Staphylococcus aureus (bacteria), (gene. exp.) Mus musculus (house mouse)
Gene: Prkaca, Pkaca / Production host: Escherichia coli (E. coli) / References: UniProt: P05132, cAMP-dependent protein kinase

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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: 5.55 Å3/Da / Density % sol: 77.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 5.5 / Details: 91mM MES pH 5.5, 2.33M Na formate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.38→50 Å / Num. obs: 31056 / % possible obs: 99.7 % / Redundancy: 6.5 % / Net I/σ(I): 13.7
Reflection shellResolution: 3.38→3.52 Å / Redundancy: 6.1 % / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UOY, 2M5A, 4NTS

4uoy

2m5a

4nts


Resolution: 3.38→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.939 / SU B: 42.478 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22732 1493 4.8 %RANDOM
Rwork0.19 ---
obs0.1918 29563 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 135.845 Å2
Baniso -1Baniso -2Baniso -3
1--4.43 Å20 Å2-0 Å2
2--2.03 Å20 Å2
3---2.4 Å2
Refinement stepCycle: 1 / Resolution: 3.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6616 0 0 0 6616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196757
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9659139
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3885840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.71424.578308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.409151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8081535
X-RAY DIFFRACTIONr_chiral_restr0.0890.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215094
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_it6.4797.2953366
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.05610.9534204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.9647.4383389
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.29327990
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.11236755
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded26.48856616
LS refinement shellResolution: 3.384→3.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 113 -
Rwork0.302 1927 -
obs--88.89 %
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)
11.3526-0.12250.34851.581-0.03611.97350.06450.34980.3156-0.35440.02730.2266-0.3016-0.2996-0.09180.27730.02920.02340.18470.11670.1398-7.2206-61.1492-27.1028
25.1798-0.89931.63062.536-0.47243.38740.30450.2874-1.149-0.5410.1129-0.09151.003-0.0788-0.41741.15610.0235-0.20450.51690.35871.035-61.0229-53.6584-56.8724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 44
2X-RAY DIFFRACTION1A45 - 227
3X-RAY DIFFRACTION1A228 - 336
4X-RAY DIFFRACTION1A337 - 410
5X-RAY DIFFRACTION1A411 - 501
6X-RAY DIFFRACTION2B107 - 170
7X-RAY DIFFRACTION2B171 - 278
8X-RAY DIFFRACTION2B279 - 455

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