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PDBsum entry 1rwa

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protein ligands metals links
Lyase PDB id
1rwa
Jmol
Contents
Protein chain
754 a.a. *
Ligands
GOL ×4
Metals
_HG ×3
Waters ×1103
* Residue conservation analysis
PDB id:
1rwa
Name: Lyase
Title: Crystal structure of arthrobacter aurescens chondroitin ac l
Structure: Chondroitin ac lyase. Chain: a. Ec: 4.2.2.5
Source: Arthrobacter aurescens. Organism_taxid: 43663
Resolution:
1.30Å     R-factor:   0.134     R-free:   0.156
Authors: V.V.Lunin,Y.Li,H.Miyazono,M.Kyogashima,A.W.Bell,M.Cygler
Key ref:
V.V.Lunin et al. (2004). High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism. J Mol Biol, 337, 367-386. PubMed id: 15003453 DOI: 10.1016/j.jmb.2003.12.071
Date:
16-Dec-03     Release date:   13-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P84141  (P84141_ARTAU) -  Chondroitinase (Chondroitin lyase)
Seq:
Struc:
 
Seq:
Struc:
757 a.a.
754 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     extracellular region   1 term 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     catalytic activity     5 terms  

 

 
DOI no: 10.1016/j.jmb.2003.12.071 J Mol Biol 337:367-386 (2004)
PubMed id: 15003453  
 
 
High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism.
V.V.Lunin, Y.Li, R.J.Linhardt, H.Miyazono, M.Kyogashima, T.Kaneko, A.W.Bell, M.Cygler.
 
  ABSTRACT  
 
Chondroitin lyases (EC 4.2.2.4 and EC 4.2.2.5) are glycosaminoglycan-degrading enzymes that act as eliminases. Chondroitin lyase AC from Arthrobacter aurescens (ArthroAC) is known to act on chondroitin 4-sulfate and chondroitin 6-sulfate but not on dermatan sulfate. Like other chondroitin AC lyases, it is capable of cleaving hyaluronan. We have determined the three-dimensional crystal structure of ArthroAC in its native form as well as in complex with its substrates (chondroitin 4-sulfate tetrasaccharide, CS(tetra) and hyaluronan tetrasaccharide) at resolution varying from 1.25 A to 1.9A. The primary sequence of ArthroAC has not been previously determined but it was possible to determine the amino acid sequence of this enzyme from the high-resolution electron density maps and to confirm it by mass spectrometry. The enzyme-substrate complexes were obtained by soaking the substrate into the crystals for varying lengths of time (30 seconds to ten hours) and flash-cooling the crystals. The electron density map for crystals soaked in the substrate for as short as 30 seconds showed the substrate clearly and indicated that the ring of central glucuronic acid assumes a distorted boat conformation. This structure strongly supports the lytic mechanism where Tyr242 acts as a general base that abstracts the proton from the C5 position of glucuronic acid while Asn183 and His233 neutralize the charge on the glucuronate acidic group. Comparison of this structure with that of chondroitinase AC from Flavobacterium heparinum (FlavoAC) provides an explanation for the exolytic and endolytic mode of action of ArthroAC and FlavoAC, respectively.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. (a) Stereo view of the superposition of the C^a traces of ArthroAC (blue) and SpHL (1EGU) (red); (b) overlay of oligosaccharide substrates from ArthroAC (blue), FlavoAC(Y234F) (1HMW, magenta) and SpHL(Y408F) (1LXK, green) based on the superposition of the backbone of active site Asn, His, Tyr (Phe) and Arg residues. The Figure was prepared with programs sPDBv[51.] and POV-Ray(TM) (http://www.povray.org/).
Figure 6.
Figure 6. Stereo view of the conformation of the 460-469 loop in native and complexed ArthroAC (blue) and in ArthroAC-Hg (magenta). The location of the thimerosal Hg atom near the Cys408 in the open conformation is shown as a magenta ball. The side-chains of His233, Arg296, Glu407 and Trp465 are shown explicitly with the hydrogen bonds marked in broken lines. The +2 and +1 sugars are also shown.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 337, 367-386) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287626 Z.H.Elmabrouk, F.Vincent, M.Zhang, N.L.Smith, J.P.Turkenburg, S.J.Charnock, G.W.Black, and E.J.Taylor (2011).
Crystal structures of a family 8 polysaccharide lyase reveal open and highly occluded substrate-binding cleft conformations.
  Proteins, 79, 965-974.
PDB codes: 2wco 2wda 2x03
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
20552664 T.V.Vuong, and D.B.Wilson (2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
  Biotechnol Bioeng, 107, 195-205.  
19193638 A.Ochiai, T.Itoh, B.Mikami, W.Hashimoto, and K.Murata (2009).
Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases.
  J Biol Chem, 284, 10181-10189.
PDB codes: 2zux 2zuy
19004833 B.Pacheco, M.Maccarana, D.R.Goodlett, A.Malmström, and L.Malmström (2009).
Identification of the Active Site of DS-epimerase 1 and Requirement of N-Glycosylation for Enzyme Function.
  J Biol Chem, 284, 1741-1747.  
18849565 V.Prabhakar, I.Capila, V.Soundararajan, R.Raman, and R.Sasisekharan (2009).
Recombinant Expression, Purification, and Biochemical Characterization of Chondroitinase ABC II from Proteus vulgaris.
  J Biol Chem, 284, 974-982.  
18163177 G.J.Sathisha, Y.K.Prakash, V.B.Chachadi, N.N.Nagaraja, S.R.Inamdar, D.D.Leonidas, H.S.Savithri, and B.M.Swamy (2008).
X-ray sequence ambiguities of Sclerotium rolfsii lectin resolved by mass spectrometry.
  Amino Acids, 35, 309-320.  
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
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
16893885 T.Itoh, W.Hashimoto, B.Mikami, and K.Murata (2006).
Crystal structure of unsaturated glucuronyl hydrolase complexed with substrate: molecular insights into its catalytic reaction mechanism.
  J Biol Chem, 281, 29807-29816.
PDB codes: 2ahf 2ahg 2d5j
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
15501829 A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, and N.C.Strynadka (2005).
Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate.
  J Biol Chem, 280, 2105-2115.
PDB codes: 1xsi 1xsj 1xsk
16314578 N.L.Smith, E.J.Taylor, A.M.Lindsay, S.J.Charnock, J.P.Turkenburg, E.J.Dodson, G.J.Davies, and G.W.Black (2005).
Structure of a group A streptococcal phage-encoded virulence factor reveals a catalytically active triple-stranded beta-helix.
  Proc Natl Acad Sci U S A, 102, 17652-17657.
PDB code: 2c3f
15155751 G.Michel, K.Pojasek, Y.Li, T.Sulea, R.J.Linhardt, R.Raman, V.Prabhakar, R.Sasisekharan, and M.Cygler (2004).
The structure of chondroitin B lyase complexed with glycosaminoglycan oligosaccharides unravels a calcium-dependent catalytic machinery.
  J Biol Chem, 279, 32882-32896.
PDB codes: 1ofl 1ofm
15341727 S.S.Rajan, X.Yang, F.Collart, V.L.Yip, S.G.Withers, A.Varrot, J.Thompson, G.J.Davies, and W.F.Anderson (2004).
Novel catalytic mechanism of glycoside hydrolysis based on the structure of an NAD+/Mn2+ -dependent phospho-alpha-glucosidase from Bacillus subtilis.
  Structure, 12, 1619-1629.
PDB code: 1u8x
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.