The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution

Lietzke, S. E.; Scavetta, Robert D.; Yoder, Marilyn D.; Jurnak, Frances

doi:10.1104/pp.111.1.73

Cited by 59 publications

(44 citation statements)

References 54 publications

(54 reference statements)

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“…This C-terminal module (residues 327-649) had previously been expressed as a separate entity, termed Pel10Acm, and shown to be an endo-acting polygalacturonic acid lyase with activity solely against the homogalacturonic acid backbone. Catalytic activity is optimal at pH 10.3 and is absolutely dependent on Ca 2ϩ with maximal activity at Ϸ2 mM [Ca 2ϩ ] (10), as observed for many other polysaccharide lyases (6,(18)(19)(20) and supported by threedimensional analysis of enzymes from family PL-1 (3,6,(21)(22)(23).…”

Section: Pel10a Frommentioning

confidence: 81%

Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases

Charnock

Brown

Turkenburg

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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Enzyme-catalyzed ␤-elimination of sugar uronic acids, exemplified by the degradation of plant cell wall pectins, plays an important role in a wide spectrum of biological processes ranging from the recycling of plant biomass through to pathogen virulence. The three-dimensional crystal structure of the catalytic module of a ''family PL-10'' polysaccharide lyase, Pel10Acm from Cellvibrio japonicus, solved at a resolution of 1.3 Å, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the ''parallel ␤-helix'' topology. The ''Michaelis'' complex of an inactive mutant in association with the substrate trigalacturonate͞Ca 2؉ reveals the catalytic machinery harnessed by this polygalacturonate lyase, which displays a stunning resemblance, presumably through convergent evolution, to the tetragalacturonic acid complex observed for a structurally unrelated polygalacturonate lyase from family PL-1. Common coordination of the ؊1 and ؉1 subsite saccharide carboxylate groups by a protein-liganded Ca 2؉ ion, the positioning of an arginine catalytic base in close proximity to the ␣-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti-␤-elimination mechanism.

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Section: Pel10a Frommentioning

confidence: 81%

Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases

Charnock

Brown

Turkenburg

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

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“…It has a similar number of residues per helical turn to the Perutz model and the extensive backbone hydrogen bonding between the parallel ␤-sheets. Unlike the Perutz structure, however, the plant fold has a compact core that largely excludes solvent molecules and it appears to be stabilized by tracts of stacked aromatic and aliphatic groups (34,36), residue that interact in the ␤-sheet of native wild-type FBP28.…”

Section: Discussionmentioning

confidence: 99%

Rapid amyloid fiber formation from the fast-folding WW domain FBP28

Ferguson

Berriman

Petrovich

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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The WW domains are small proteins that contain a three-stranded, antiparallel ␤-sheet. The 40-residue murine FBP28 WW domain rapidly formed twirling ribbon-like fibrils at physiological temperature and pH, with morphology typical of amyloid fibrils. These ribbons were unusually wide and well ordered, making them highly suitable for structural studies. Their x-ray and electrondiffraction patterns displayed the characteristic amyloid fiber 0.47-nm reflection of the cross-␤ diffraction signature. Both conventional and electron cryomicroscopy showed clearly that the ribbons were composed of many 2.5-nm-wide subfilaments that ran parallel to the long axis of the fiber. There was a region of lower density along the center of each filament. Lateral association of these filaments generated twisted, often interlinked, sheets up to 40 nm wide and many microns in length. The pitch of the helix varied from 60 to 320 nm, depending on the width of the ribbon. The wild-type FBP28 fibers were formed under conditions in which multiexponential folding kinetics is observed in other studies and which was attributed to a change in the mechanism of folding. It is more likely that those phases result from initial events in the off-pathway aggregation observed here.esolving how a protein folds and unfolds is not only a challenge in itself, but is very important for understanding protein misfolding and associated diseases, such as spongiform encephalopathy and amyloidoses (1, 2). The complex nature of protein folding requires a multidisciplinary approach, combining kinetics, structural analysis, and computer simulation. Recently, there has been increasing synergy between conclusions drawn from experimental models of fast-folding proteins and those from molecular dynamics simulation (3-6), suggesting that an accurate atomic-level description of protein folding, unfolding, and misfolding is now a realistic prospect (7).The ultrafast-folding WW domain proteins (6, 8) are ubiquitous in eukaryotes and are involved in cellular signaling, vesicular trafficking, and have been implicated in a number of disease pathologies (9). WW domains are typically 35-45 residues long and adopt a three-stranded, antiparallel ␤-sheet topology (Fig. 1), with conserved tryptophan residues at the N and C termini (10-13). These small domains follow a two-state transition in both equilibrium and kinetic experiments (6,8). Further, there is surprisingly good agreement between molecular dynamics simulations and experiments for a number of WW domain homologues, with the emerging consensus being that folding is rate limited by formation of a ␤-hairpin (4, 6), although it has been suggested that this mechanism can be modulated by changes in temperature (6).A recent study (14) proposes that folding of the murine FBP28 WW domain is a multistate, unimolecular reaction with formation of a populated intermediate during folding. They suggest that changes in temperature or sequence can modulate the folding pathway from three-to two-state. These results are in contrast to our ...

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“…The BsPel has three aspartic acid residues in the putative active site cleft: Asp184 is a ligand to the putative active site calcium ion, the others being Asp223 and 227. PelE has three Asps also at the active site but PelC has two Asps and a Glu, and the cleft is not so pronounced (Lietzke et al, 1994(Lietzke et al, , 1996Pickersgill et al, 1994;Yoder et al, 1993). In ZePel, the putative active site is more basic than in pectin lyases due to the contributions of Lys227, Arg262 and Arg264 (as in BsPel).…”

Section: Isolation and Analysis Of Zinnia Pectate Lyase Cdnamentioning

confidence: 99%

A pectate lyase from Zinnia elegans is auxin inducible

et al. 1998

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SummaryThe Zinnia mesophyll cell system consists of isolated leaf mesophyll cells in culture that can be induced, by auxin and cytokinin, to reproducibly trans-differentiate into tracheary elements (TE) after 96 h, while in the presence of auxin alone the cells simply elongate. In a search for genes involved in modifications to cell-wall architecture before any overt signs of cell differentiation, a differential hybridization of a 72-h cDNA library with probes from mRNA at time-points of 24 h and 72 h was done revealing a number of transcripts up-regulated between these times. One of these cDNAs shows homology to pectate lyase, a pectin-degrading enzyme. The complete cDNA sequence (ZePel) corresponds to a translated protein of 44 kDa with an N-terminal signal peptide of about 2 kDa, and one potential N-glycosylation site. Northern analysis confirms that the strong expression of this gene during TE induction occurs at a very early stage of the process and is due solely to the presence of auxin in the induction medium. In situ hybridization studies in young Zinnia stems show that ZePel expression is associated with vascular bundles and shoot primordia. Recombinant protein made in Escherichia coli possesses calcium-dependent pectate lyase activity. Pectate lyase activity is detected in elongating and differentiating in vitro cell populations. The role of this enzyme in remodelling the cell wall during cell elongation and differentiation is discussed.

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The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution

Abstract: The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the enterobacteria Erwinia cbrysanfbemi has been refined by molecular dynamics techniques to a resolution of 2.2 a and an R factor (an agreement factor between observed structure factor amplitudes) of

Cited by 59 publications

References 54 publications

Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases

Convergent evolution sheds light on the anti-β-elimination mechanism common to family 1 and 10 polysaccharide lyases

Rapid amyloid fiber formation from the fast-folding WW domain FBP28

A pectate lyase from Zinnia elegans is auxin inducible

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