First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.

3ij9

From Proteopedia

Jump to: navigation, search


3ij9, resolution 1.85Å ()
Ligands: , , , ,
Non-Standard Residues:
Gene: AMY2A (Homo sapiens)
Activity: Alpha-amylase, with EC number 3.2.1.1
Related: 3ij7, 3ij8
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Contents

Directed 'in situ' Elongation as a Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic a-Amylase

Publication Abstract from PubMed

While covalent catalytic intermediates of retaining alpha-transglycosylases have been structurally characterized previously, no such information for a hydrolytic alpha-amylase has been obtained. This study presents a new "in situ" enzymatic elongation methodology that, for the first time, has allowed the isolation and structural characterization of a catalytically competent covalent glycosyl-enzyme intermediate with human pancreatic alpha-amylase. This has been achieved by the use of a 5-fluoro-beta-l-idosyl fluoride "warhead" in conjunction with either alpha-maltotriosyl fluoride or 4'-O-methyl-alpha-maltosyl fluoride as elongation agents. This generates an oligosaccharyl-5-fluoroglycosyl fluoride that then reacts with the free enzyme. The resultant covalent intermediates are extremely stable, with hydrolytic half-lives on the order of 240 h for the trisaccharide complex. In the presence of maltose, however, they undergo turnover via transglycosylation according to a half-life of less than 1 h. Structural studies of intermediate complexes unambiguously show the covalent attachment of a 5-fluoro-alpha-l-idosyl moiety in the chair conformation to the side chain of the catalytic nucleophile D197. The elongated portions of the intermediate complexes are found to bind in the high-affinity -2 and -3 binding subsites, forming extensive hydrogen-bonding interactions. Comparative structural analyses with the related noncovalent complex formed by acarbose highlight the structural rigidity of the enzyme surface during catalysis and the key role that substrate conformational flexibility must play in this process. Taken together, the structural data provide atomic details of several key catalytic steps. The scope of this elongation approach to probe the active sites and catalytic mechanisms of alpha-amylases is further demonstrated through preliminary experiments with porcine pancreatic alpha-amylase.

Directed "in Situ" Inhibitor Elongation as a Strategy To Structurally Characterize the Covalent Glycosyl-Enzyme Intermediate of Human Pancreatic alpha-Amylase (,)., Zhang R, Li C, Williams LK, Rempel BP, Brayer GD, Withers SG, Biochemistry. 2009 Oct 15. PMID:19803533

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3ij9 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA.

See Also

Reference

  • Zhang R, Li C, Williams LK, Rempel BP, Brayer GD, Withers SG. Directed "in Situ" Inhibitor Elongation as a Strategy To Structurally Characterize the Covalent Glycosyl-Enzyme Intermediate of Human Pancreatic alpha-Amylase (,). Biochemistry. 2009 Oct 15. PMID:19803533 doi:10.1021/bi901400p

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools