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- PDB-1hm2: ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 1hm2
TitleACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS
ComponentsCHONDROITINASE AC
KeywordsLYASE / protein-oligosaccharide complex / active site / catalysis
Function / homology
Function and homology information


chondroitin AC lyase / chondroitin AC lyase activity / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 ...Polysaccharide lyase 8 / Polysaccharide lyase 8, N-terminal alpha-helical / Polysaccharide lyase family 8, N terminal alpha-helical domain / Polysaccharide lyase family 8, C-terminal / Polysaccharide lyase family 8, C-terminal beta-sandwich domain / Polysaccharide lyase family 8, central domain / Polysaccharide lyase family 8, super-sandwich domain / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Chondroitinase Ac; Chain A, domain 3 / Polysaccharide lyase family 8-like, C-terminal / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPedobacter heparinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHuang, W. / Boju, L. / Tkalec, L. / Su, H. / Yang, H.O. / Gunay, N.S. / Linhardt, R.J. / Kim, Y.S. / Matte, A. / Cygler, M.
CitationJournal: Biochemistry / Year: 2001
Title: Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
Authors: Huang, W. / Boju, L. / Tkalec, L. / Su, H. / Yang, H.O. / Gunay, N.S. / Linhardt, R.J. / Kim, Y.S. / Matte, A. / Cygler, M.
History
DepositionDec 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Data collection / Derived calculations
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHONDROITINASE AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0725
Polymers79,7981
Non-polymers2,2744
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.900, 86.900, 192.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CHONDROITINASE AC


Mass: 79797.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pedobacter heparinus (bacteria) / Production host: Pedobacter heparinus (bacteria) / References: UniProt: Q59288, chondroitin AC lyase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide 2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)- ...2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 794.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucp[2Me]b1-4DXylpb1-4DGlcpAa1-2[LRhapa1-4]DManpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,5,4/[a1122h-1a_1-5][a2122A-1a_1-5][a212h-1b_1-5][a1221m-1b_1-5_2*OC][a2211m-1a_1-5]/1-2-3-4-5/a2-b1_a4-e1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-Manp]{[(2+1)][a-D-GlcpA]{[(4+1)][b-D-Xylp]{[(4+1)][a-L-Fucp2Me]{}}}[(4+1)][b-L-Rhap]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 502.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAa1-2[LRhapa1-4]DManpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5][a2122A-1a_1-5][a2211m-1a_1-5]/1-2-3/a2-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-Manp]{[(2+1)][a-D-GlcpA]{}[(4+1)][a-L-Rhap]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha- ...alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose


Type: oligosaccharide / Mass: 936.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LIdopAa1-3DGalpNAc[4S]b1-4LIdopAa1-3DGalpNAc[4S]b1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2112h-1b_1-5_2*NCC/3=O_4*OSO/3=O/3=O][a2121A-1a_1-5]/1-2-1-2/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc4SO3]{[(3+1)][a-L-IdopA]{[(4+1)][b-D-GalpNAc4SO3]{[(3+1)][a-L-IdopA]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 314 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, sodium acetate, hepes , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG33501reservoir
2400 mmsodium acetate1reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 1999 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 48610 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.2 Å / Rmerge(I) obs: 0.244 / % possible all: 87.2
Reflection
*PLUS
Num. measured all: 204934
Reflection shell
*PLUS
% possible obs: 87.6 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.27 1627 random
Rwork0.233 --
all-47131 -
obs-47131 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5382 0 148 313 5843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.42

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