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PDBsum entry 1qaz

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Lyase PDB id
1qaz
Jmol
Contents
Protein chain
351 a.a. *
Ligands
SO4 ×2
Waters ×298
* Residue conservation analysis
PDB id:
1qaz
Name: Lyase
Title: Crystal structure of alginate lyase a1-iii from sphingomonas species a1 at 1.78a resolution
Structure: Protein (alginate lyase a1-iii). Chain: a. Engineered: yes
Source: Sphingomonas sp.. Organism_taxid: 28214. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Biol. unit: Monomer (from PDB file)
Resolution:
1.78Å     R-factor:   0.180     R-free:   0.233
Authors: H.-J.Yoon
Key ref:
H.J.Yoon et al. (1999). Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution. J Mol Biol, 290, 505-514. PubMed id: 10390348 DOI: 10.1006/jmbi.1999.2883
Date:
08-Apr-99     Release date:   19-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9KWU1  (Q9KWU1_SPHSX) -  Alginate lyase
Seq:
Struc:
 
Seq:
Struc:
641 a.a.
351 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biochemical function     lyase activity     1 term  

 

 
DOI no: 10.1006/jmbi.1999.2883 J Mol Biol 290:505-514 (1999)
PubMed id: 10390348  
 
 
Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.
H.J.Yoon, B.Mikami, W.Hashimoto, K.Murata.
 
  ABSTRACT  
 
The three-dimensional structure of alginate lyase A1-III (ALYIII) from a Sphingomonas species A1 was determined by X-ray crystallography. The enzyme was crystallized by the hanging-drop vapour-diffusion method in the presence of 49% ammonium sulfate at 20 degrees C. The crystals are monoclinic and belong to the space group C2 with unit cell dimensions of a=49.18 A, b=93.08 A, c=82.10 A and beta=104.12 degrees. There was one molecule of alginate lyase in the asymmetric unit of the crystal. The diffraction data up to 1. 71 A were collected with Rsymof 5.0%. The crystal structure of ALYIII was solved by the multiple isomorphous replacement method and refined at 1.78 A resolution using X-PLOR with a final R -factor of 18.0% for 10.0 to 1.78 A resolution data. The refined model of ALYIII contained 351 amino acid residues, 299 water molecules and two sulfate ions. The three-dimensional structure of ALYIII was abundant in helices and had a deep tunnel-like cleft in a novel (alpha6/alpha5)-barrel structure, which was similar to the (alpha6/alpha6)-barrel found in glucoamylase and cellulase. This structure presented the possibility that alginate molecules might penetrate into the cleft to interact with the catalytic site of ALYIII.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Overall structure of the ALYIII ribbon stereo-diagram. The Figure shows loops (red), 12 a-helices (blue), two sulfate ions (green), and two S-S bridges, Cys49 - Cys112 and Cys188 - Cys189 (yel- low). The 12 a-helices are num- bered from the N-terminal. The bound sulfate ions and the cystine residues are represented as ball- and-sticks. The Figure was pre- pared using the programs MOL- SCRIPT (Kraulis, 1991) and RASTER3D (Merrit & Murphy, 1994).
Figure 10.
Figure 10. Structural comparison of a-helices within the a/a-barrel structure of ALYIII (blue), gluco- amylase (yellow) and cellulase (pink). The superimposed result is shown as a schematic view in C a -traces of a-helices. The co- ordinates of glucoamylase (1DOG) and cellulase (1CEM) were taken from the Brookhaven Protein Data Bank.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 290, 505-514) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18574239 H.J.Rozeboom, T.M.Bjerkan, K.H.Kalk, H.Ertesvåg, S.Holtan, F.L.Aachmann, S.Valla, and B.W.Dijkstra (2008).
Structural and Mutational Characterization of the Catalytic A-module of the Mannuronan C-5-epimerase AlgE4 from Azotobacter vinelandii.
  J Biol Chem, 283, 23819-23828.
PDB codes: 2pyg 2pyh
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.  
17947240 A.Ochiai, T.Itoh, Y.Maruyama, A.Kawamata, B.Mikami, W.Hashimoto, and K.Murata (2007).
A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER.
  J Biol Chem, 282, 37134-37145.
PDB codes: 2z8r 2z8s
  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.  
16521140 C.S.Rye, A.Matte, M.Cygler, and S.G.Withers (2006).
An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase.
  Chembiochem, 7, 631-637.  
16565082 D.Shaya, A.Tocilj, Y.Li, J.Myette, G.Venkataraman, R.Sasisekharan, and M.Cygler (2006).
Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product.
  J Biol Chem, 281, 15525-15535.
PDB codes: 2fuq 2fut
15901714 M.T.Albrecht, and N.L.Schiller (2005).
Alginate lyase (AlgL) activity is required for alginate biosynthesis in Pseudomonas aeruginosa.
  J Bacteriol, 187, 3869-3872.  
  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.  
15632283 Z.Zhang, S.Kochhar, and M.G.Grigorov (2005).
Descriptor-based protein remote homology identification.
  Protein Sci, 14, 431-444.  
14997549 I.Hudáky, Z.Gáspári, O.Carugo, M.Cemazar, S.Pongor, and A.Perczel (2004).
Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations.
  Proteins, 55, 152-168.  
15136569 M.Yamasaki, S.Moriwaki, O.Miyake, W.Hashimoto, K.Murata, and B.Mikami (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.
PDB code: 1vav
15148314 T.Itoh, S.Akao, W.Hashimoto, B.Mikami, and K.Murata (2004).
Crystal structure of unsaturated glucuronyl hydrolase, responsible for the degradation of glycosaminoglycan, from Bacillus sp. GL1 at 1.8 A resolution.
  J Biol Chem, 279, 31804-31812.
PDB code: 1vd5
  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.  
14523022 D.J.Rigden, and M.J.Jedrzejas (2003).
Structures of Streptococcus pneumoniae hyaluronate lyase in complex with chondroitin and chondroitin sulfate disaccharides. Insights into specificity and mechanism of action.
  J Biol Chem, 278, 50596-50606.
PDB codes: 1ojm 1ojn 1ojo 1ojp
12833544 D.J.Rigden, and M.J.Jedrzejas (2003).
Genome-based identification of a carbohydrate binding module in Streptococcus pneumoniae hyaluronate lyase.
  Proteins, 52, 203-211.  
12775688 M.Gimmestad, H.Sletta, H.Ertesvåg, K.Bakkevig, S.Jain, S.J.Suh, G.Skjåk-Braek, T.E.Ellingsen, D.E.Ohman, and S.Valla (2003).
The Pseudomonas fluorescens AlgG protein, but not its mannuronan C-5-epimerase activity, is needed for alginate polymer formation.
  J Bacteriol, 185, 3515-3523.  
12719417 M.S.Akhtar, and V.Bhakuni (2003).
Streptococcus pneumoniae hyaluronate lyase contains two non-cooperative independent folding/unfolding structural domains: characterization of functional domain and inhibitors of enzyme.
  J Biol Chem, 278, 25509-25516.  
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.  
15224891 P.Michaud, A.Da Costa, B.Courtois, and J.Courtois (2003).
Polysaccharide lyases: recent developments as biotechnological tools.
  Crit Rev Biotechnol, 23, 233-266.  
12475987 W.Hashimoto, H.Nankai, B.Mikami, and K.Murata (2003).
Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan.
  J Biol Chem, 278, 7663-7673.
PDB codes: 1j0m 1j0n
11786996 M.Hartmann, O.B.Holm, G.A.Johansen, G.Skjåk-Braek, and B.T.Stokke (2002).
Mode of action of recombinant Azotobacter vinelandii mannuronan C-5 epimerases AlgE2 and AlgE4.
  Biopolymers, 63, 77-88.  
11157235 W.Hashimoto, H.Miki, N.Tsuchiya, H.Nankai, and K.Murata (2001).
Polysaccharide lyase: molecular cloning, sequencing, and overexpression of the xanthan lyase gene of Bacillus sp. strain GL1.
  Appl Environ Microbiol, 67, 713-720.  
11676004 W.Hashimoto, K.Momma, Y.Mishima, B.Mikami, and K.Murata (2001).
Super-channel in bacteria: function and structure of a macromolecule import system mediated by a pit-dependent ABC transporter.
  Biosci Biotechnol Biochem, 65, 1949-1956.  
11327856 W.Huang, L.Boju, L.Tkalec, H.Su, H.O.Yang, N.S.Gunay, R.J.Linhardt, Y.S.Kim, A.Matte, and M.Cygler (2001).
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
  Biochemistry, 40, 2359-2372.
PDB codes: 1hm2 1hm3 1hmu 1hmw
11272816 Y.Iwamoto, R.Araki, K.Iriyama, T.Oda, H.Fukuda, S.Hayashida, and T.Muramatsu (2001).
Purification and characterization of bifunctional alginate lyase from Alteromonas sp. strain no. 272 and its action on saturated oligomeric substrates.
  Biosci Biotechnol Biochem, 65, 133-142.  
11029455 L.A.Preston, T.Y.Wong, C.L.Bender, and N.L.Schiller (2000).
Characterization of alginate lyase from Pseudomonas syringae pv. syringae.
  J Bacteriol, 182, 6268-6271.  
10716923 S.Li, S.J.Kelly, E.Lamani, M.Ferraroni, and M.J.Jedrzejas (2000).
Structural basis of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase.
  EMBO J, 19, 1228-1240.
PDB code: 1egu
11018131 T.Y.Wong, L.A.Preston, and N.L.Schiller (2000).
ALGINATE LYASE: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications.
  Annu Rev Microbiol, 54, 289-340.  
10913091 W.Hashimoto, O.Miyake, K.Momma, S.Kawai, and K.Murata (2000).
Molecular identification of oligoalginate lyase of Sphingomonas sp. strain A1 as one of the enzymes required for complete depolymerization of alginate.
  J Bacteriol, 182, 4572-4577.  
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.