1RWH

Crystal structure of Arthrobacter aurescens chondroitin AC lyase in complex with chondroitin tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

High-resolution crystal structure of Arthrobacter aurescens chondroitin AC lyase: an enzyme-substrate complex defines the catalytic mechanism

Lunin, V.V.Li, Y.Linhardt, R.J.Miyazono, H.Kyogashima, M.Kaneko, T.Bell, A.W.Cygler, M.

(2004) J Mol Biol 337: 367-386

  • DOI: 10.1016/j.jmb.2003.12.071
  • Primary Citation of Related Structures:  
    1RW9, 1RWA, 1RWC, 1RWF, 1RWG, 1RWH

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, and Montréal Joint Centre for Structural Biology, Montréal, Québec, 6100 Royalmount Ave., Montréal, Québec, Canada H4P 2R2.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
chondroitin AC lyaseA757Paenarthrobacter aurescensMutation(s): 0 
EC: 4.2.2.5
UniProt
Find proteins for P84141 (Paenarthrobacter aurescens)
Explore P84141 
Go to UniProtKB:  P84141
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP84141
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-2,6-anhydro-3-deoxy-L-xylo-hexonic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranoseB 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14354FC
GlyCosmos:  G14354FC
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.114 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.621α = 90
b = 86.305β = 106.95
c = 80.514γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Version format compliance
  • Version 1.3: 2012-05-09
    Changes: Other
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary