PDBsum entry 1vav

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Lyase PDB id
Protein chains
222 a.a. *
Waters ×298
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of alginate lyase pa1167 from pseudomonas at 2.0 a resolution
Structure: Alginate lyase pa1167. Chain: a, b. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 208964. Strain: pao1. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.00Å     R-factor:   0.187     R-free:   0.240
Authors: M.Yamasaki,S.Moriwaki,O.Miyake,W.Hashimoto,K.Murata,B.Mikami
Key ref:
M.Yamasaki et al. (2004). Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold. J Biol Chem, 279, 31863-31872. PubMed id: 15136569 DOI: 10.1074/jbc.M402466200
19-Feb-04     Release date:   25-May-04    
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Protein chains
Pfam   ArchSchema ?
Q9I4H0  (Q9I4H0_PSEAE) -  Uncharacterized protein
223 a.a.
222 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M402466200 J Biol Chem 279:31863-31872 (2004)
PubMed id: 15136569  
Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.
M.Yamasaki, S.Moriwaki, O.Miyake, W.Hashimoto, K.Murata, B.Mikami.
Structural and functional analyses of alginate lyases are important in the clarification of the biofilm-dependent ecosystem in Pseudomonas aeruginosa and in the development of therapeutic agents for bacterial disease. Most alginate lyases are classified into polysaccharide lyase (PL) family-5 and -7 based on their primary structures. Family PL-7 enzymes are still poorly characterized especially in structural properties. Among family PL-7, a gene coding for a hypothetical protein (PA1167) homologous to Sphingomonas alginate lyase A1-II was found to be present in the P. aeruginosa genome. PA1167 overexpressed in Escherichia coli cleaved glycosidic bonds in alginate and released unsaturated saccharides, indicating that PA1167 is an alginate lyase catalyzing a beta-elimination reaction. The enzyme acted preferably on heteropolymeric regions endolytically and worked most efficiently at pH 8.5 and 40 degrees C. The specific activity of PA1167, however, was much weaker than that of the known alginate lyase AlgL, suggesting that AlgL plays a main role in alginate depolymerization in P. aeruginosa. In addition to this specific activity, differences were found between PA1167 and AlgL in enzyme properties such as molecular mass, optimum pH, salt effect, and substrate specificity. The first crystal structure of the family PL-7 alginate lyase was determined at 2.0 A resolution. PA1167 was found to form a glove-like beta-sandwich composed of 15 beta-strands and 3 alpha-helices. The structural difference between the beta-sandwich PA1167 of family PL-7 and alpha/alpha-barrel AlgL of family PL-5 may be responsible for the enzyme characteristics. Crystal structures of polysaccharide lyases determined so far indicate that they can be assigned to three folding groups having parallel beta-helix, alpha/alpha-barrel, and alpha/alpha-barrel + antiparallel beta-sheet structures as basic frames. PA1167 is the fourth novel folding structure found among polysaccharide lyases.
  Selected figure(s)  
Figure 1.
FIG. 1. Block sites of alginate polymer and alginate lyase reactions. A, MM; B, GG; C, MG block sites. M and G represent -D-mannuronate and -L-guluronate. Vertical arrows indicate cleavage sites for alginate lyase reactions and horizontal arrows indicate those for reactions. D, reaction scheme for the TBA method.
Figure 5.
FIG. 5. Crystal structure of PA1167. A, overall structure of PA1167 (stereo diagram). B, topology diagram. -Sheets in A are shown in yellow and B in orange.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 31863-31872) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19941025 K.Uchimura, M.Miyazaki, Y.Nogi, T.Kobayashi, and K.Horikoshi (2010).
Cloning and sequencing of alginate lyase genes from deep-sea strains of Vibrio and Agarivorans and characterization of a new Vibrio enzyme.
  Mar Biotechnol (NY), 12, 526-533.  
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
19482920 M.Gimmestad, H.Ertesvåg, T.M.Heggeset, O.Aarstad, B.I.Svanem, and S.Valla (2009).
Characterization of three new Azotobacter vinelandii alginate lyases, one of which is involved in cyst germination.
  J Bacteriol, 191, 4845-4853.  
18978091 N.Konno, K.Igarashi, N.Habu, M.Samejima, and A.Isogai (2009).
Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family.
  Appl Environ Microbiol, 75, 101-107.  
19002649 T.Kobayashi, K.Uchimura, M.Miyazaki, Y.Nogi, and K.Horikoshi (2009).
A new high-alkaline alginate lyase from a deep-sea bacterium Agarivorans sp.
  Extremophiles, 13, 121-129.  
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.  
17166279 A.K.Arakaki, W.Tian, and J.Skolnick (2006).
High precision multi-genome scale reannotation of enzyme function by EFICAz.
  BMC Genomics, 7, 315.  
  16682783 A.Ochiai, M.Yamasaki, B.Mikami, W.Hashimoto, and K.Murata (2006).
Crystallization and preliminary X-ray analysis of an exotype alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, a member of polysaccharide lyase family 15.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 486-488.  
16776680 H.J.Jeong, S.A.Lee, P.D.Moon, H.J.Na, R.K.Park, J.Y.Um, H.M.Kim, and S.H.Hong (2006).
Alginic acid has anti-anaphylactic effects and inhibits inflammatory cytokine expression via suppression of nuclear factor-kappaB activation.
  Clin Exp Allergy, 36, 785-794.  
17057348 J.Vasur, R.Kawai, A.M.Larsson, K.Igarashi, M.Sandgren, M.Samejima, and J.Ståhlberg (2006).
X-ray crystallographic native sulfur SAD structure determination of laminarinase Lam16A from Phanerochaete chrysosporium.
  Acta Crystallogr D Biol Crystallogr, 62, 1422-1429.
PDB code: 2cl2
16549009 R.I.Sadreyev, and N.V.Grishin (2006).
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.
  BMC Struct Biol, 6, 6.  
  16511020 M.Yamasaki, K.Ogura, S.Moriwaki, W.Hashimoto, K.Murata, and B.Mikami (2005).
Crystallization and preliminary X-ray analysis of alginate lyases A1-II and A1-II' from Sphingomonas sp. A1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 288-290.  
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.  
  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.  
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 code is shown on the right.