PDBsum entry 1pif

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Glycosyltransferase PDB id
Protein chain
496 a.a.
Waters ×278

References listed in PDB file
Key reference
Title Carbohydrate and protein-Based inhibitors of porcine pancreatic alpha-Amylase: structure analysis and comparison of their binding characteristics.
Authors M.Machius, L.Vértesy, R.Huber, G.Wiegand.
Ref. J Mol Biol, 1996, 260, 409-421. [DOI no: 10.1006/jmbi.1996.0410]
PubMed id 8757803
The crystal structures of porcine pancreatic alpha-amylase isozyme II (PPA II) in its free form and complexed with the trestatin A derived pseudo-octasaccharide V-1532 have been determined using Patterson search techniques at resolutions of 2.3 and 2.2 angstroms, respectively. Seven rings of the competitive inhibitor V-1532 could be detected in the active site region as well as two maltose units in secondary binding sites on the surface. V-1532 occupies the five central sugar binding subsites similar to the PPA/acarbose structure. A sixth ring exists at the reducing end, connecting two symmetry related PPA molecules. The seventh moiety, a 6-hydroxymethylconduritol ring, is located at the non-reducing end. The electron density for this ring is relatively weak, indicating considerable disorder. This study shows that PPA is able to accommodate more than five rings in the active site region, but that additional rings would increase the binding affinity only slightly, which is in accordance with kinetic experiments. A comparison of the structures of free PPA, PPA/V-1532 and PPA/Tendamistat shows the characteristic conformational changes that accompany inhibitor binding and distinguish pseudo-oligosaccharide inhibitors from proteinaceous inhibitors. Although both classes of inhibitors block the sugar binding subsites in the active site region, the extreme specificity and binding affinity of the proteinaceous inhibitors is probably due to an intricate interaction pattern involving areas further away from the catalytic center.
Figure 2.
Figure 2. Stereo drawings (programme MOLSCRIPT, Kraulis, 1992) showing the active site region. PPA side-chains involved in binding to both inhibitors are held in blue, side-chains involved exclusively in V-1532 binding in green, and side-chains involved exclusively in Tendamistat binding in red. a, Free PPA; b, PPA complexed with V-1532; the 6-hydroxymethylconduritol ring in subsite 0 is held in grey, symmetry related PPA side-chains interacting with the glucose ring in subsite 6 in green with black atoms, and the maltose molecules in the secondary binding sites as well as the interacting side-chains in PPA in yellow and black, respectively; c, PPA complexed with Tendamistat; seg- ment 1, pink; segment 2, blue; segment 3, yellow; segment 4, black.
Figure 6.
Figure 6. Superposition of the region around residues 305 to 308 showing the different conformations in free PPA (red), PPA/V-1532 (green), and PPA/Tendamistat (pink).
The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 260, 409-421) copyright 1996.
Secondary reference #1
Title The crystal structure of porcine pancreatic alpha-Amylase in complex with the microbial inhibitor tendamistat.
Authors G.Wiegand, O.Epp, R.Huber.
Ref. J Mol Biol, 1995, 247, 99.
PubMed id 7897663
Secondary reference #2
Title Carbohydrate binding sites in a pancreatic alpha-Amylase-Substrate complex, Derived from x-Ray structure analysis at 2.1 a resolution.
Authors M.Qian, R.Haser, F.Payan.
Ref. Protein Sci, 1995, 4, 747-755. [DOI no: 10.1002/pro.5560040414]
PubMed id 7613472
Full text Abstract
Figure 5.
Fig. 5. Stackingfeature between theplane of te tryptophan ring f residue 388 andthehydropho- bicregionofthemaltoseunitboundatthe ``sec- ondsite'' of theenzyme molecule. Dottedsurface representsthevanderWaalsradiioftheatoms.
Figure 7.
Fig. 7. Detailed stereo view of the arrangement of protein sidechainsinvolved in with the monosaccharide. Calcium ion is in with the sugar unit through its water ligand.
The above figures are reproduced from the cited reference which is an Open Access publication published by the Protein Society
Secondary reference #3
Title Refined molecular structure of pig pancreatic alpha-Amylase at 2.1 a resolution.
Authors S.B.Larson, A.Greenwood, D.Cascio, J.Day, A.Mcpherson.
Ref. J Mol Biol, 1994, 235, 1560-1584.
PubMed id 8107092
Secondary reference #4
Title The active center of a mammalian alpha-Amylase. Structure of the complex of a pancreatic alpha-Amylase with a carbohydrate inhibitor refined to 2.2-A resolution.
Authors M.Qian, R.Haser, G.Buisson, E.Duée, F.Payan.
Ref. Biochemistry, 1994, 33, 6284-6294. [DOI no: 10.1021/bi00186a031]
PubMed id 8193143
Full text Abstract
Secondary reference #5
Title Structure and molecular model refinement of pig pancreatic alpha-Amylase at 2.1 a resolution.
Authors M.Qian, R.Haser, F.Payan.
Ref. J Mol Biol, 1993, 231, 785-799.
PubMed id 8515451
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