1U4J

Crystal structure of a carbohydrate induced dimer of group I phospholipase A2 from Bungarus caeruleus at 2.1 A resolution

Summary for 1U4J

• Entry DOI: 10.2210/pdb1u4j/pdb
• Related: 1FE5
• Descriptor: phospholipase A2 isoform 2, SODIUM ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: phospholipase a2, homodimer, bungarus caeruleus, mannose, hydrolase
• Biological source: Bungarus caeruleus
• Cellular location: Secreted: Q6SLM1
• Total number of polymer chains: 2
• Total formula weight: 26618.61

Authors

Singh, G.,Gourinath, S.,Sharma, S.,Bhanumathi, S.,Betzel, C.,Srinivasan, A.,Singh, T.P. (deposition date: 2004-07-26, release date: 2004-08-10, Last modification date: 2024-11-13)

Primary citation

Singh, G.,Gourinath, S.,Sarvanan, K.,Sharma, S.,Bhanumathi, S.,Betzel, C.,Yadav, S.,Srinivasan, A.,Singh, T.P.
Crystal structure of a carbohydrate induced homodimer of phospholipase A(2) from Bungarus caeruleus at 2.1A resolution
J.Struct.Biol., 149:264-272, 2005

PubMed Abstract: This is the first crystal structure of a carbohydrate induced dimer of phospholipase A(2) (PLA(2)). This is an endogenous complex formed between two PLA(2) molecules and two mannoses. It was isolated from Krait venom (Bungarus caeruleus) and crystallized as such. The complete amino acid sequence of PLA(2) was determined using cDNA method. Three-dimensional structure of the complex has been solved with molecular replacement method and refined to a final R-factor of 0.192 for all the data in the resolution range 20.0-2.1A. The presence of mannose molecules in the protein crystals was confirmed using dinitrosalicylic acid test and the molecular weight of the dimer was verified with MALDI-TOF. As indicated by dynamic light scattering and analytical ultracentrifugation the dimer was also stable in solution. The good quality non-protein electron density at the interface of two PLA(2) molecules enabled us to model two mannoses. The mannoses are involved extensively in interactions with protein atoms of both PLA(2) molecules. Some of the critical amino acid residues such as Asp 49 and Tyr 31, which are part of the substrate-binding site, are found facing the interface and interacting with mannoses. The structure of the complex clearly shows that the dimerization is caused by mannoses and it results in the loss of enzymatic activity.

PubMed: 15721580
DOI: 10.1016/j.jsb.2004.11.011

Experimental method

X-RAY DIFFRACTION (2.18 Å)