1y75
From Proteopedia
(New page: 200px<br /><applet load="1y75" size="450" color="white" frame="true" align="right" spinBox="true" caption="1y75, resolution 2.30Å" /> '''A new form of cataly...) |
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| - | [[Image:1y75.gif|left|200px]]<br /><applet load="1y75" size=" | + | [[Image:1y75.gif|left|200px]]<br /><applet load="1y75" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1y75, resolution 2.30Å" /> | caption="1y75, resolution 2.30Å" /> | ||
'''A new form of catalytically inactive phospholipase A2 with an unusual disulphide bridge Cys 32- Cys 49 reveals recognition for N-acetylglucosmine'''<br /> | '''A new form of catalytically inactive phospholipase A2 with an unusual disulphide bridge Cys 32- Cys 49 reveals recognition for N-acetylglucosmine'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja | + | The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja naja sagittifera reveals the presence of a new PLA2-like protein with eight disulphide bridges. The heterodimer is formed between a commonly observed group I PLA2 having seven characteristic disulfide bonds and a novel PLA2-like protein (Cys-PLA2) containing two extra cysteines at two highly conserved sites (positions 32 and 49) of structural and functional importance. The crystals of the heterodimer belong to tetragonal space group P41212 with cell dimensions, a = b = 77.7 A and c = 68.4 A corresponding to a solvent content of 33%, which is one of the lowest values observed so far in the PLA2 crystals. The structure has been solved with molecular replacement method and refined to a final R value of 21.6% [Rfree = 25.6%]. The electron density revealed the presence of cysteines 32 and 49 that are covalently linked to give rise to an eighth disulphide bridge in the PLA2-like monomer. A non-protein high-quality electron density was also observed at the substrate-binding site in the PLA2-like protein that has been interpreted as N-acetylglucosamine. The overall tertiary folds of the two monomers are similar having all features of PLA2-type folding. A zinc ion is detected at the interface of the heterodimer with fivefold coordination while another zinc ion was found on the surface of Cys-PLA2 with sixfold coordination. The conformations of the calcium-binding loops of both monomers are significantly different from each other as well as from those in other group I PLA2s. The N-acetylglucosamine molecule is favorably placed in the substrate-binding site of Cys-PLA2 and forms five hydrogen bonds and several van der Waals interactions with protein atoms, thus indicating a strong affinity. It also provides clue of the possible mechanism of sugar recognition by PLA2 and PLA2-like proteins. The formation of heterodimer seems to have been induced by zinc ion. |
==About this Structure== | ==About this Structure== | ||
| - | 1Y75 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Naja_sagittifera Naja sagittifera] with NAG and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] Full crystallographic information is available from [http:// | + | 1Y75 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Naja_sagittifera Naja sagittifera] with <scene name='pdbligand=NAG:'>NAG</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phospholipase_A(2) Phospholipase A(2)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.4 3.1.1.4] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y75 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Sharma, S.]] | [[Category: Sharma, S.]] | ||
[[Category: Singh, N.]] | [[Category: Singh, N.]] | ||
| - | [[Category: Singh, R | + | [[Category: Singh, R K.]] |
| - | [[Category: Singh, T | + | [[Category: Singh, T P.]] |
[[Category: Srinivasan, A.]] | [[Category: Srinivasan, A.]] | ||
[[Category: NAG]] | [[Category: NAG]] | ||
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[[Category: molecular association]] | [[Category: molecular association]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:02:23 2008'' |
Revision as of 14:02, 21 February 2008
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A new form of catalytically inactive phospholipase A2 with an unusual disulphide bridge Cys 32- Cys 49 reveals recognition for N-acetylglucosmine
Overview
The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja naja sagittifera reveals the presence of a new PLA2-like protein with eight disulphide bridges. The heterodimer is formed between a commonly observed group I PLA2 having seven characteristic disulfide bonds and a novel PLA2-like protein (Cys-PLA2) containing two extra cysteines at two highly conserved sites (positions 32 and 49) of structural and functional importance. The crystals of the heterodimer belong to tetragonal space group P41212 with cell dimensions, a = b = 77.7 A and c = 68.4 A corresponding to a solvent content of 33%, which is one of the lowest values observed so far in the PLA2 crystals. The structure has been solved with molecular replacement method and refined to a final R value of 21.6% [Rfree = 25.6%]. The electron density revealed the presence of cysteines 32 and 49 that are covalently linked to give rise to an eighth disulphide bridge in the PLA2-like monomer. A non-protein high-quality electron density was also observed at the substrate-binding site in the PLA2-like protein that has been interpreted as N-acetylglucosamine. The overall tertiary folds of the two monomers are similar having all features of PLA2-type folding. A zinc ion is detected at the interface of the heterodimer with fivefold coordination while another zinc ion was found on the surface of Cys-PLA2 with sixfold coordination. The conformations of the calcium-binding loops of both monomers are significantly different from each other as well as from those in other group I PLA2s. The N-acetylglucosamine molecule is favorably placed in the substrate-binding site of Cys-PLA2 and forms five hydrogen bonds and several van der Waals interactions with protein atoms, thus indicating a strong affinity. It also provides clue of the possible mechanism of sugar recognition by PLA2 and PLA2-like proteins. The formation of heterodimer seems to have been induced by zinc ion.
About this Structure
1Y75 is a Protein complex structure of sequences from Naja sagittifera with and as ligands. Active as Phospholipase A(2), with EC number 3.1.1.4 Full crystallographic information is available from OCA.
Reference
Crystal structure of a heterodimer of phospholipase A2 from Naja naja sagittifera at 2.3 A resolution reveals the presence of a new PLA2-like protein with a novel cys 32-Cys 49 disulphide bridge with a bound sugar at the substrate-binding site., Jabeen T, Singh N, Singh RK, Jasti J, Sharma S, Kaur P, Srinivasan A, Singh TP, Proteins. 2006 Feb 1;62(2):329-37. PMID:16287060
Page seeded by OCA on Thu Feb 21 16:02:23 2008
Categories: Naja sagittifera | Phospholipase A(2) | Protein complex | Betzel, C. | Jabeen, T. | Jasti, J. | Kaur, P. | Perbandt, M. | Sharma, S. | Singh, N. | Singh, R K. | Singh, T P. | Srinivasan, A. | NAG | ZN | Activity | Enzyme | Molecular association
