The crystal structure of a novel, inactive, lysine 49 PLA2 from Agkistrodon acutus venom: an ultrahigh resolution, AB initio structure determination.
The crystal structure of acutohaemolysin, a lysine 49 phospholipase A2 protein with 1010 non-hydrogen protein atoms and 232 water molecules, has been determined ab initio using the program SnB at an ultrahigh resolution of 0.8 A. The lack of catalytic activity appears to be related to the presence of Phe102, which prevents the access of substrate to the active site. The substitution of tryptophan for leucine at residue 10 interferes with dimer formation and may be responsible for the additional loss of hemolytic activity. The ultrahigh resolution of the experimental diffraction data permits alternative conformations to be modeled for disordered residues, many hydrogen atoms to be located, the protonation of the Nepsilon2 atom in the catalytic residue His48 to be observed experimentally, and the density of the bonding electrons to be analyzed in detail.
Liu
Qun
Q
Key Laboratory of Structural Biology, Chinese Academy of Sciences, China.
Huang
Qingqiu
Q
Teng
Maikun
M
Weeks
Charles M
CM
Jelsch
Christian
C
Zhang
Rongguang
R
Niu
Liwen
L
D017836:Agkistrodon; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D019281:Dimerization; D006460:Hemolysin Proteins / Q000737:chemistry; D006859:Hydrogen / Q000737:chemistry; D006860:Hydrogen Bonding; D008239:Lysine / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010649:Phenylalanine / Q000737:chemistry; D010741:Phospholipases A / Q000378:metabolism*; D054467:Phospholipases A2; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D012910:Snake Venoms / Q000378:metabolism*; D014364:Tryptophan / Q000737:chemistry
D006460:Hemolysin Proteins; D012910:Snake Venoms; D010649:Phenylalanine; D006859:Hydrogen; D014364:Tryptophan; D010741:Phospholipases A; D054467:Phospholipases A2; D008239:Lysine