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PDBsum entry 1poc
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.1.1.4
- phospholipase A2.
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Reaction:
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a 1,2-diacyl-sn-glycero-3-phosphocholine + H2O = a 1-acyl-sn-glycero-3- phosphocholine + a fatty acid + H+
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1,2-diacyl-sn-glycero-3-phosphocholine
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+
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H2O
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=
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1-acyl-sn-glycero-3- phosphocholine
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+
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fatty acid
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+
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H(+)
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Cofactor:
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Ca(2+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Science
250:1563-1566
(1990)
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PubMed id:
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Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue.
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D.L.Scott,
Z.Otwinowski,
M.H.Gelb,
P.B.Sigler.
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ABSTRACT
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The 2.0 angstroms crystal structure of a complex containing bee-venom
phospholipase A2 (PLA2) and a phosphonate transition-state analogue was solved
by multiple isomorphous replacement. The electron-density map is sufficiently
detailed to visualize the proximal sugars of the enzyme's N-linked carbohydrate
and a single molecule of the transition-state analogue bound ot its active
center. Although bee-venom PLA2 does not belong to the large homologous Class
I/II family that encompasses most other well-studied PLA2s, there is segmental
sequence similarity and conservation of many functional substructures.
Comparison of the bee-venom enzyme with other phospholipase structures provides
compelling evidence for a common catalytic mechanism.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Karray,
F.Frikha,
Y.Ben Ali,
Y.Gargouri,
and
S.Bezzine
(2011).
Purification and biochemical characterization of a secreted group IIA chicken intestinal phospholipase A2.
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Lipids Health Dis,
10,
27.
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A.Więckowska,
E.Jabłonowska,
E.Rogalska,
and
R.Bilewicz
(2011).
Structuring of supported hybrid phospholipid bilayers on electrodes with phospholipase A2.
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Phys Chem Chem Phys,
13,
9716-9724.
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J.I.dos Santos,
M.Cintra-Francischinelli,
R.J.Borges,
C.A.Fernandes,
P.Pizzo,
A.C.Cintra,
A.S.Braz,
A.M.Soares,
and
M.R.Fontes
(2011).
Structural, functional, and bioinformatics studies reveal a new snake venom homologue phospholipase Aâ‚‚ class.
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Proteins,
79,
61-78.
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PDB code:
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G.Ofek,
K.McKee,
Y.Yang,
Z.Y.Yang,
J.Skinner,
F.J.Guenaga,
R.Wyatt,
M.B.Zwick,
G.J.Nabel,
J.R.Mascola,
and
P.D.Kwong
(2010).
Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining region.
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J Virol,
84,
2955-2962.
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L.R.Shen,
M.H.Ding,
L.W.Zhang,
W.G.Zhang,
L.Liu,
and
D.Li
(2010).
Expression of a bee venom phospholipase A2 from Apis cerana cerana in the baculovirus-insect cell.
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J Zhejiang Univ Sci B,
11,
342-349.
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P.Haimi,
M.Hermansson,
K.C.Batchu,
J.A.Virtanen,
and
P.Somerharju
(2010).
Substrate efflux propensity plays a key role in the specificity of secretory A-type phospholipases.
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J Biol Chem,
285,
751-760.
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A.Jerga,
D.J.Miller,
S.W.White,
and
C.O.Rock
(2009).
Molecular determinants for interfacial binding and conformational change in a soluble diacylglycerol kinase.
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J Biol Chem,
284,
7246-7254.
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A.Karray,
F.Frikha,
A.Ben Bacha,
Y.Ben Ali,
Y.Gargouri,
and
S.Bezzine
(2009).
Biochemical and molecular characterization of purified chicken pancreatic phospholipase A2.
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FEBS J,
276,
4545-4554.
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E.A.Aragão,
P.Randazzo-Moura,
S.Rostelato-Ferreira,
L.Rodrigues-Simioni,
and
R.J.Ward
(2009).
Shared structural determinants for the calcium-independent liposome membrane permeabilization and sarcolemma depolarization in Bothropstoxin-I, a LYS49-PLA(2) from the venom of Bothrops jararacussu.
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Int J Biochem Cell Biol,
41,
2588-2593.
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J.E.Guy,
U.Ståhl,
and
Y.Lindqvist
(2009).
Crystal structure of a class XIB phospholipase A2 (PLA2): rice (oryza sativa) isoform-2 pla2 and an octanoate complex.
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J Biol Chem,
284,
19371-19379.
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PDB codes:
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J.H.Baek,
T.H.Woo,
C.B.Kim,
J.H.Park,
H.Kim,
S.Lee,
and
S.H.Lee
(2009).
Differential gene expression profiles in the venom gland/sac of Orancistrocerus drewseni (Hymenoptera: Eumenidae).
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Arch Insect Biochem Physiol,
71,
205-222.
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M.Merchant,
R.Heard,
and
C.Monroe
(2009).
Characterization of phospholipase A(2) activity in serum of the American alligator (Alligator mississippiensis).
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J Exp Zool A Ecol Genet Physiol,
311,
662-666.
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L.Linderoth,
T.L.Andresen,
K.Jørgensen,
R.Madsen,
and
G.H.Peters
(2008).
Molecular basis of phospholipase A2 activity toward phospholipids with sn-1 substitutions.
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Biophys J,
94,
14-26.
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S.J.Melton,
and
S.J.Landry
(2008).
Three dimensional structure directs T-cell epitope dominance associated with allergy.
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Clin Mol Allergy,
6,
9.
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Y.Markert,
J.Mansfeld,
A.Schierhorn,
K.P.Rücknagel,
and
R.Ulbrich-Hofmann
(2007).
Production of synthetically created phospholipase A(2) variants with industrial impact.
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Biotechnol Bioeng,
98,
48-59.
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N.Singh,
T.Jabeen,
A.Pal,
S.Sharma,
M.Perbandt,
C.Betzel,
and
T.P.Singh
(2006).
Crystal structures of the complexes of a group IIA phospholipase A2 with two natural anti-inflammatory agents, anisic acid, and atropine reveal a similar mode of binding.
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Proteins,
64,
89.
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PDB codes:
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F.Karamloo,
P.Schmid-Grendelmeier,
F.Kussebi,
M.Akdis,
M.Salagianni,
B.R.von Beust,
A.Reimers,
J.Zumkehr,
L.Soldatova,
Z.Housley-Markovic,
U.Müller,
T.Kündig,
D.M.Kemeny,
M.D.Spangfort,
K.Blaser,
and
C.A.Akdis
(2005).
Prevention of allergy by a recombinant multi-allergen vaccine with reduced IgE binding and preserved T cell epitopes.
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Eur J Immunol,
35,
3268-3276.
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G.Singh,
J.Jasti,
K.Saravanan,
S.Sharma,
P.Kaur,
A.Srinivasan,
and
T.P.Singh
(2005).
Crystal structure of the complex formed between a group I phospholipase A2 and a naturally occurring fatty acid at 2.7 A resolution.
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Protein Sci,
14,
395-400.
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PDB code:
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J.H.Li,
C.X.Zhang,
L.R.Shen,
Z.H.Tang,
and
J.A.Cheng
(2005).
Expression and regulation of phospholipase A2 in venom gland of the chinese honeybee, Apis cerana cerana.
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Arch Insect Biochem Physiol,
60,
1.
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M.Markova,
R.A.Koratkar,
K.A.Silverman,
V.E.Sollars,
M.MacPhee-Pellini,
R.Walters,
J.P.Palazzo,
A.M.Buchberg,
L.D.Siracusa,
and
S.A.Farber
(2005).
Diversity in secreted PLA2-IIA activity among inbred mouse strains that are resistant or susceptible to Apc Min/+ tumorigenesis.
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Oncogene,
24,
6450-6458.
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T.Jabeen,
S.Sharma,
N.Singh,
R.K.Singh,
P.Kaur,
M.Perbandt,
C.h.Betzel,
A.Srinivasan,
and
T.P.Singh
(2005).
Crystal structure of a calcium-induced dimer of two isoforms of cobra phospholipase A2 at 1.6 A resolution.
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Proteins,
59,
856-863.
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PDB codes:
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C.Buhot,
A.Chenal,
A.Sanson,
S.Pouvelle-Moratille,
M.H.Gelb,
A.Ménez,
D.Gillet,
and
B.Maillère
(2004).
Alteration of the tertiary structure of the major bee venom allergen Api m 1 by multiple mutations is concomitant with low IgE reactivity.
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Protein Sci,
13,
2970-2978.
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D.J.Rigden,
L.W.Hwa,
S.Marangoni,
M.H.Toyama,
and
I.Polikarpov
(2003).
The structure of the D49 phospholipase A2 piratoxin III from Bothrops pirajai reveals unprecedented structural displacement of the calcium-binding loop: possiblerelationship to cooperative substrate binding.
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Acta Crystallogr D Biol Crystallogr,
59,
255-262.
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PDB code:
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D.Marsh
(2003).
Lipid-binding proteins: structure of the phospholipid ligands.
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Protein Sci,
12,
2109-2117.
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H.Zhao,
and
P.K.Kinnunen
(2003).
Modulation of the activity of secretory phospholipase A2 by antimicrobial peptides.
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Antimicrob Agents Chemother,
47,
965-971.
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J.Pei,
and
N.V.Grishin
(2002).
Breaking the singleton of germination protease.
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| |
Protein Sci,
11,
691-697.
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U.R.Müller
(2002).
Recombinant Hymenoptera venom allergens.
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| |
Allergy,
57,
570-576.
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A.H.de Oliveira,
J.R.Giglio,
S.H.Andrião-Escarso,
A.S.Ito,
and
R.J.Ward
(2001).
A pH-induced dissociation of the dimeric form of a lysine 49-phospholipase A2 abolishes Ca2+-independent membrane damaging activity.
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Biochemistry,
40,
6912-6920.
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A.Pomés,
and
M.D.Chapman
(2001).
Can knowledge of the molecular structure of allergens improve immunotherapy?
|
| |
Curr Opin Allergy Clin Immunol,
1,
549-554.
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R.A.Steiner,
H.J.Rozeboom,
A.de Vries,
K.H.Kalk,
G.N.Murshudov,
K.S.Wilson,
and
B.W.Dijkstra
(2001).
X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution.
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Acta Crystallogr D Biol Crystallogr,
57,
516-526.
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PDB code:
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S.A.Tatulian
(2001).
Toward understanding interfacial activation of secretory phospholipase A2 (PLA2): membrane surface properties and membrane-induced structural changes in the enzyme contribute synergistically to PLA2 activation.
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| |
Biophys J,
80,
789-800.
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W.H.Lee,
M.T.da Silva Giotto,
S.Marangoni,
M.H.Toyama,
I.Polikarpov,
and
R.C.Garratt
(2001).
Structural basis for low catalytic activity in Lys49 phospholipases A2--a hypothesis: the crystal structure of piratoxin II complexed to fatty acid.
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Biochemistry,
40,
28-36.
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PDB code:
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A.Dessen
(2000).
Phospholipase A(2) enzymes: structural diversity in lipid messenger metabolism.
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Structure,
8,
R15-R22.
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E.Valentin,
and
G.Lambeau
(2000).
Increasing molecular diversity of secreted phospholipases A(2) and their receptors and binding proteins.
|
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Biochim Biophys Acta,
1488,
59-70.
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I.Krizaj,
and
F.Gubensek
(2000).
Neuronal receptors for phospholipases A(2 )and beta-neurotoxicity.
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Biochimie,
82,
807-814.
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M.Falconi,
A.Desideri,
and
S.Rufini
(2000).
Membrane-perturbing activity of Viperidae myotoxins: an electrostatic surface potential approach to a puzzling problem.
|
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J Mol Recognit,
13,
14-19.
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P.Bała,
P.Grochowski,
K.Nowiński,
B.Lesyng,
and
J.A.McCammon
(2000).
Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).
|
| |
Biophys J,
79,
1253-1262.
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A.Kettner,
H.Henry,
G.J.Hughes,
G.Corradin,
and
F.Spertini
(1999).
IgE and T-cell responses to high-molecular weight allergens from bee venom.
|
| |
Clin Exp Allergy,
29,
394-401.
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C.Yuan,
and
M.Tsai
(1999).
Pancreatic phospholipase A(2): new views on old issues.
|
| |
Biochim Biophys Acta,
1441,
215-222.
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D.E.Timm,
H.A.Mueller,
P.Bhanumoorthy,
J.M.Harp,
and
G.J.Bunick
(1999).
Crystal structure and mechanism of a carbon-carbon bond hydrolase.
|
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Structure,
7,
1023-1033.
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PDB codes:
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G.Ollesch,
A.Kaunzinger,
D.Juchelka,
M.Schubert-Zsilavecz,
and
U.Ermler
(1999).
Phospholipid bound to the flavohemoprotein from Alcaligenes eutrophus.
|
| |
Eur J Biochem,
262,
396-405.
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I.Ubarretxena-Belandia,
R.C.Cox,
R.Dijkman,
M.R.Egmond,
H.M.Verheij,
and
N.Dekker
(1999).
Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.
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Eur J Biochem,
260,
794-800.
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J.W.Simons,
M.D.van Kampen,
I.Ubarretxena-Belandia,
R.C.Cox,
C.M.Alves dos Santos,
M.R.Egmond,
and
H.M.Verheij
(1999).
Identification of a calcium binding site in Staphylococcus hyicus lipase: generation of calcium-independent variants.
|
| |
Biochemistry,
38,
2.
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M.H.Gelb,
W.Cho,
and
D.C.Wilton
(1999).
Interfacial binding of secreted phospholipases A(2): more than electrostatics and a major role for tryptophan.
|
| |
Curr Opin Struct Biol,
9,
428-432.
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M.R.Barnes,
R.B.Russell,
R.R.Copley,
C.P.Ponting,
P.Bork,
S.Cumberledge,
F.Reichsman,
and
H.M.Moore
(1999).
A lipid-binding domain in Wnt: a case of mistaken identity?
|
| |
Curr Biol,
9,
R717-R719.
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P.G.Hains,
P.A.Ramsland,
and
K.W.Broady
(1999).
Modeling of acanthoxin A1, a PLA2 enzyme from the venom of the common death adder (Acanthophis antarcticus).
|
| |
Proteins,
35,
80-88.
|
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C.A.Akdis,
T.Blesken,
D.Wymann,
M.Akdis,
and
K.Blaser
(1998).
Differential regulation of human T cell cytokine patterns and IgE and IgG4 responses by conformational antigen variants.
|
| |
Eur J Immunol,
28,
914-925.
|
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D.Wymann,
C.A.Akdis,
T.Blesken,
M.Akdis,
R.Crameri,
and
K.Blaser
(1998).
Enzymatic activity of soluble phospholipase A2 does not affect the specific IgE, IgG4 and cytokine responses in bee sting allergy.
|
| |
Clin Exp Allergy,
28,
839-849.
|
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F.Ghomashchi,
Y.Lin,
M.S.Hixon,
B.Z.Yu,
R.Annand,
M.K.Jain,
and
M.H.Gelb
(1998).
Interfacial recognition by bee venom phospholipase A2: insights into nonelectrostatic molecular determinants by charge reversal mutagenesis.
|
| |
Biochemistry,
37,
6697-6710.
|
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I.Ubarretxena-Belandia,
J.W.Boots,
H.M.Verheij,
and
N.Dekker
(1998).
Role of the cofactor calcium in the activation of outer membrane phospholipase A.
|
| |
Biochemistry,
37,
16011-16018.
|
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K.Sekar,
A.Kumar,
X.Liu,
M.D.Tsai,
M.H.Gelb,
and
M.Sundaralingam
(1998).
Structure of the complex of bovine pancreatic phospholipase A2 with a transition-state analogue.
|
| |
Acta Crystallogr D Biol Crystallogr,
54,
334-341.
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PDB code:
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L.Lichtenbergova,
E.T.Yoon,
and
W.Cho
(1998).
Membrane penetration of cytosolic phospholipase A2 is necessary for its interfacial catalysis and arachidonate specificity.
|
| |
Biochemistry,
37,
14128-14136.
|
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M.T.da Silva Giotto,
R.C.Garratt,
G.Oliva,
Y.P.Mascarenhas,
J.R.Giglio,
A.C.Cintra,
W.F.de Azevedo,
R.K.Arni,
and
R.J.Ward
(1998).
Crystallographic and spectroscopic characterization of a molecular hinge: conformational changes in bothropstoxin I, a dimeric Lys49-phospholipase A2 homologue.
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| |
Proteins,
30,
442-454.
|
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B.Z.Yu,
F.Ghomashchi,
Y.Cajal,
R.R.Annand,
O.G.Berg,
M.H.Gelb,
and
M.K.Jain
(1997).
Use of an imperfect neutral diluent and outer vesicle layer scooting mode hydrolysis to analyze the interfacial kinetics, inhibition, and substrate preferences of bee venom phospholipase A2.
|
| |
Biochemistry,
36,
3870-3881.
|
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|
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J.M.Carballido,
A.Faith,
N.Carballido-Perrig,
and
K.Blaser
(1997).
The intensity of T cell receptor engagement determines the cytokine pattern of human allergen-specific T helper cells.
|
| |
Eur J Immunol,
27,
515-521.
|
|
|
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|
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K.Sekar,
B.Z.Yu,
J.Rogers,
J.Lutton,
X.Liu,
X.Chen,
M.D.Tsai,
M.K.Jain,
and
M.Sundaralingam
(1997).
Phospholipase A2 engineering. Structural and functional roles of the highly conserved active site residue aspartate-99.
|
| |
Biochemistry,
36,
3104-3114.
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PDB codes:
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K.Sekar,
S.Eswaramoorthy,
M.K.Jain,
and
M.Sundaralingam
(1997).
Crystal structure of the complex of bovine pancreatic phospholipase A2 with the inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero-2-phosphomethanol,.
|
| |
Biochemistry,
36,
14186-14191.
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PDB code:
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S.M.McHugh
(1997).
To bee or not to be? T-cell responses to bee venom PLA2 in relation to anaphylaxis and immunotherapy.
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Clin Exp Allergy,
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Comparison of the antibody response to bee venom phospholipase A2 induced by natural exposure in humans or by immunization in mice.
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Phosphatidylinositol-specific phospholipase C cyclic phosphodiesterase activity depends on solvent polarity.
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Ammodytoxin C gene helps to elucidate the irregular structure of Crotalinae group II phospholipase A2 genes.
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Eur J Biochem,
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R.R.Annand,
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Active site of bee venom phospholipase A2: the role of histidine-34, aspartate-64 and tyrosine-87.
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Biochemistry,
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Overview on denominated allergens.
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Clin Exp Allergy,
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NMR structures of phospholipase A2 reveal conformational changes during interfacial activation.
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Nat Struct Biol,
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R.W.Schevitz,
N.J.Bach,
D.G.Carlson,
N.Y.Chirgadze,
D.K.Clawson,
R.D.Dillard,
S.E.Draheim,
L.W.Hartley,
N.D.Jones,
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(1995).
Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2.
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| |
Nat Struct Biol,
2,
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PDB codes:
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Z.S.Derewenda
(1995).
A twist in the tale of lipolytic enzymes.
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Nat Struct Biol,
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Proc Natl Acad Sci U S A,
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PDB code:
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K.B.Glaser,
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Bee venom phospholipase A2-specific T cell clones from human allergic and non-allergic individuals: cytokine patterns change in response to the antigen concentration.
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Metal-binding sites in proteins.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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