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Structural features of the Nostoc punctiforme debranching enzyme reveal the basis of its mechanism and substrate specificity.

Dumbrepatil AB, Choi JH, Park JT, Kim MJ, Kim TJ, Woo EJ, Park KH
Proteins 78 348-56 (2010)
Related entries: 2wc7, 2wcs

Cited: 8 times
EuropePMC logo PMID: 19768689

Abstract

The debranching enzyme Nostoc punctiforme debranching enzyme (NPDE) from the cyanobacterium Nostoc punctiforme (PCC73102) hydrolyzes the alpha-1,6 glycosidic linkages of malto-oligosaccharides. Despite its high homology to cyclodextrin/pullulan (CD/PUL)-hydrolyzing enzymes from glycosyl hydrolase 13 family (GH-13), NPDE exhibits a unique catalytic preference for longer malto-oligosaccharides (>G8), performing hydrolysis without the transgylcosylation or CD-hydrolyzing activities of other GH-13 enzymes. To investigate the molecular basis for the property of NPDE, we determined the structure of NPDE at 2.37-A resolution. NPDE lacks the typical N-terminal domain of other CD/PUL-hydrolyzing enzymes and forms an elongated dimer in a head-to-head configuration. The unique orientation of residues 25-55 in NPDE yields an extended substrate binding groove from the catalytic center to the dimeric interface. The substrate binding groove with a lengthy cavity beyond the -1 subsite exhibits a suitable architecture for binding longer malto-oligosaccharides (>G8). These structural results may provide a molecular basis for the substrate specificity and catalytic function of this cyanobacterial enzyme, distinguishing it from the classical neopullulanases and CD/PUL-hydrolyzing enzymes.

Reviews citing this publication (1)

  1. Structure and function of α-glucan debranching enzymes. Møller MS, Henriksen A, Svensson B. Cell Mol Life Sci 73 2619-2641 (2016)

Articles citing this publication (7)

  1. Structural rationale for the short branched substrate specificity of the glycogen debranching enzyme GlgX. Song HN, Jung TY, Park JT, Park BC, Myung PK, Boos W, Woo EJ, Park KH. Proteins 78 1847-1855 (2010)
  2. The role of N1 domain on the activity, stability, substrate specificity and raw starch binding of amylopullulanase of the extreme thermophile Geobacillus thermoleovorans. Nisha M, Satyanarayana T. Appl Microbiol Biotechnol 99 5461-5474 (2015)
  3. Domain evolution in enzymes of the neopullulanase subfamily. Kuchtová A, Janeček Š. Microbiology (Reading) 162 2099-2115 (2016)
  4. Identification and characterization of a novel alkaline α‑amylase Amy703 belonging to a new clade from Bacillus pseudofirmus. Lu Z, Tian C, Li A, Zhang G, Ma Y. J Ind Microbiol Biotechnol 41 783-793 (2014)
  5. Reaction kinetics of substrate transglycosylation catalyzed by TreX of Sulfolobus solfataricus and effects on glycogen breakdown. Nguyen DH, Park JT, Shim JH, Tran PL, Oktavina EF, Nguyen TL, Lee SJ, Park CS, Li D, Park SH, Stapleton D, Lee JS, Park KH. J Bacteriol 196 1941-1949 (2014)
  6. A Novel Subfamily GH13_46 of the α-Amylase Family GH13 Represented by the Cyclomaltodextrinase from Flavobacterium sp. No. 92. Mareček F, Janeček Š. Molecules 27 8735 (2022)
  7. Structural features of a bacterial cyclic α-maltosyl-(1→6)-maltose (CMM) hydrolase critical for CMM recognition and hydrolysis. Kohno M, Arakawa T, Ota H, Mori T, Nishimoto T, Fushinobu S. J Biol Chem 293 16874-16888 (2018)


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