PDBsum entry 1gxm

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Lyase PDB id
Protein chains
324 a.a. *
GOL ×4
Waters ×835
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Family 10 polysaccharide lyase from cellvibrio cellulosa
Structure: Pectate lyase. Chain: a, b. Fragment: catalytic module, residues 327-649. Synonym: polygalacturonic acid lyase. Engineered: yes
Source: Cellvibrio cellulosa. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: de3.
1.32Å     R-factor:   0.132     R-free:   0.162
Authors: S.J.Charnock,I.E.Brown,J.P.Turkenburg,G.W.Black,G.J.Davies
Key ref:
S.J.Charnock et al. (2002). Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc Natl Acad Sci U S A, 99, 12067-12072. PubMed id: 12221284 DOI: 10.1073/pnas.182431199
08-Apr-02     Release date:   04-Oct-02    
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Protein chains
Pfam   ArchSchema ?
Q9F7L3  (Q9F7L3_9GAMM) -  Pectate lyase
649 a.a.
324 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)


DOI no: 10.1073/pnas.182431199 Proc Natl Acad Sci U S A 99:12067-12072 (2002)
PubMed id: 12221284  
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
S.J.Charnock, I.E.Brown, J.P.Turkenburg, G.W.Black, G.J.Davies.
Enzyme-catalyzed beta-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 A, reveals a new polysaccharide lyase fold and is the first example of a polygalacturonic acid lyase that does not exhibit the "parallel beta-helix" topology. The "Michaelis" complex of an inactive mutant in association with the substrate trigalacturonate/Ca2+ 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 Ca2+ ion, the positioning of an arginine catalytic base in close proximity to the alpha-carbon hydrogen and numerous other conserved enzyme-substrate interactions, considered in light of mutagenesis data for both families, suggest a generic polysaccharide anti-beta-elimination mechanism.
  Selected figure(s)  
Figure 3.
Fig 3. Schematic diagram of the interactions of the mutant D389A Pel10Acm with trigalacturonate. The approximate location of Asp389 from the native structure is indicated for reference.
Figure 4.
Fig 4. (a) More O'Ferral diagram for -elimination of galacto-configured uronic acids. (b) Putative E1cb/asynchronous E2 reaction mechanism for Pel10 and related enzymes in which proton abstraction by arginine is followed by leaving-group elimination. The essential role of Asp389 may involve a role in binding a second Ca^2+ ion as observed in Pel1C.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20596756 S.Basu, A.Roy, A.Ghosh, A.Bera, D.Chattopadhyay, and K.Chakrabarti (2011).
Arg²³⁵ is an essential catalytic residue of Bacillus pumilus DKS1 pectate lyase to degum ramie fibre.
  Biodegradation, 22, 153-161.  
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
20925655 V.Lombard, T.Bernard, C.Rancurel, H.Brumer, P.M.Coutinho, and B.Henrissat (2010).
A hierarchical classification of polysaccharide lyases for glycogenomics.
  Biochem J, 432, 437-444.  
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
18256495 K.Murata, S.Kawai, B.Mikami, and W.Hashimoto (2008).
Superchannel of bacteria: biological significance and new horizons.
  Biosci Biotechnol Biochem, 72, 265-277.  
17455908 Y.O.You, and W.A.van der Donk (2007).
Mechanistic investigations of the dehydration reaction of lacticin 481 synthetase using site-directed mutagenesis.
  Biochemistry, 46, 5991-6000.  
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
15849405 W.Hashimoto, K.Momma, Y.Maruyama, M.Yamasaki, B.Mikami, and K.Murata (2005).
Structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules.
  Biosci Biotechnol Biochem, 69, 673-692.  
15719022 Y.Shen, N.L.Zhukovskaya, Q.Guo, J.Florián, and W.J.Tang (2005).
Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor.
  EMBO J, 24, 929-941.
PDB codes: 1xfu 1xfv 1xfw 1xfx 1xfy 1xfz 1y0v
15159558 H.Novoa De Armas, C.Verboven, C.De Ranter, J.Desair, A.Vande Broek, J.Vanderleyden, and A.Rabijns (2004).
Azospirillum irakense pectate lyase displays a toroidal fold.
  Acta Crystallogr D Biol Crystallogr, 60, 999.
PDB code: 1r76
  16233728 W.Hashimoto, M.Yamasaki, T.Itoh, K.Momma, B.Mikami, and K.Murata (2004).
Super-channel in bacteria: structural and functional aspects of a novel biosystem for the import and depolymerization of macromolecules.
  J Biosci Bioeng, 98, 399-413.  
12876365 M.Yamasaki, S.Moriwaki, W.Hashimoto, B.Mikami, and K.Murata (2003).
Crystallization and preliminary X-ray analysis of alginate lyase, a member of family PL-7, from Pseudomonas aeruginosa.
  Acta Crystallogr D Biol Crystallogr, 59, 1499-1501.  
14553937 S.G.Walker, and M.E.Ryan (2003).
Cloning and expression of a pectate lyase from the oral spirochete Treponema pectinovorum ATCC 33768.
  FEMS Microbiol Lett, 226, 385-390.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.