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- PDB-3p2p: ENHANCED ACTIVITY AND ALTERED SPECIFICITY OF PHOSPHOLIPASE A2 BY ... -

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Basic information

Entry
Database: PDB / ID: 3p2p
TitleENHANCED ACTIVITY AND ALTERED SPECIFICITY OF PHOSPHOLIPASE A2 BY DELETION OF A SURFACE LOOP
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE(CARBOXYL ESTER)
Function / homology
Function and homology information


regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity ...regulation of D-glucose import / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / leukotriene biosynthetic process / bile acid binding / phospholipase A2 / neutrophil mediated immunity / calcium-dependent phospholipase A2 activity / positive regulation of calcium ion transport into cytosol / lipid catabolic process / neutrophil chemotaxis / positive regulation of interleukin-8 production / positive regulation of immune response / phospholipid binding / cellular response to insulin stimulus / positive regulation of fibroblast proliferation / fatty acid biosynthetic process / positive regulation of MAPK cascade / intracellular signal transduction / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phospholipase A2, major isoenzyme
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsDijkstra, B.W. / Thunnissen, M.M.G.M. / Kalk, K.H. / Drenth, J.
Citation
Journal: Science / Year: 1989
Title: Enhanced activity and altered specificity of phospholipase A2 by deletion of a surface loop.
Authors: Kuipers, O.P. / Thunnissen, M.M. / de Geus, P. / Dijkstra, B.W. / Drenth, J. / Verheij, H.M. / de Haas, G.H.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Porcine Pancreatic Phospholipase A2 at 2.6 Angstroms Resolution and Comparison with Bovine Phospholipase A2
Authors: Dijkstra, B.W. / Renetseder, R. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: The Structure of Bovine Pancreatic Prophospholipase A2 at 3.0 Angstroms Resolution
Authors: Dijkstra, B.W. / Vannes, G.J.H. / Kalk, K.H. / Brandenburg, N.P. / Hol, W.G.J. / Drenth, J.
#3: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of Bovine Pancreatic Phospholipase A2 at 1.7 Angstroms Resolution
Authors: Dijkstra, B.W. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#4: Journal: Nature / Year: 1981
Title: Active Site and Catalytic Mechanism of Phospholipase A2
Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H.
#5: Journal: J.Mol.Biol. / Year: 1978
Title: Three-Dimensional Structure and Disulfide Bond Connections in Bovine Pancreatic Phospholipase A2
Authors: Dijkstra, B.W. / Drenth, J. / Kalk, K.H. / Vandermaelen, P.J.
History
DepositionNov 29, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOLIPASE A2
B: PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9145
Polymers26,7942
Non-polymers1203
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-39 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.800, 73.400, 37.200
Angle α, β, γ (deg.)90.00, 107.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: SEE REMARK 6.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.311854, -0.931273, -0.188355), (-0.916842, 0.242941, 0.316828), (-0.249294, 0.271496, -0.929593)
Vector: 49.474, 31.477, 23.422)
DetailsTHE ENZYME CRYSTALLIZES WITH A DIMER IN THE ASYMMETRIC UNIT. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW CAN BE APPLIED TO SUBUNIT 2 (CHAIN *B*) TO OBTAIN OPTIMAL SUPERPOSITION OF C-ALPHA COORDINATES ON THOSE OF SUBUNIT 1 (CHAIN *A*). THE RMS DIFFERENCE FOR ALL 119 CARBON-ALPHA PAIRS IS 0.542 ANGSTROMS.

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13397.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00592, phospholipase A2
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsCALCIUM CA B 2 IS BOUND BETWEEN THE *A* AND *B* CHAINS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 %methanol1reservoir
2100 mMbistris1reservoir
35 mM1reservoirCaCl2

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 88.5 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.186 / Highest resolution: 2.1 Å
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 3 205 2064
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.237 / Rfactor Rwork: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: bond_d / Dev ideal: 0.009

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