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(-) Description

Title :  CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-SULFATE TETRASACCHARIDE
 
Authors :  G. Michel, M. Cygler
Date :  15 Apr 03  (Deposition) - 19 Apr 04  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Active Site, Beta-Elimination, Chondroitin 4-Sulfate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Michel, K. Pojasek, Y. Li, T. Sulea, R. Linhardt, R. Raman, V. Prabhakar, R. Sasisekharan, M. Cygler
The Structure Of Chondroitin B Lyase Complexed With Glycosaminoglycan Oligosaccharides Unravels A Calcium-Dependent Catalytic Machinery
J. Biol. Chem. V. 279 32882 2004
PubMed-ID: 15155751  |  Reference-DOI: 10.1074/JBC.M403421200

(-) Compounds

Molecule 1 - CHONDROITINASE B
    Atcc: 13125
    Chains: A
    EC Number: 4.2.2.4
    Engineered: YES
    Expression System: PEDOBACTER HEPARINUS
    Expression System Taxid: 984
    Organism Scientific: PEDOBACTER HEPARINUS
    Organism Taxid: 984
    Other Details: HYDROXY-PROLINE AT N-TERMINUS GLYCOSYLATION AT SER234

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (11, 12)

Asymmetric/Biological Unit (11, 12)
No.NameCountTypeFull Name
1ASG2Ligand/Ion2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE
2BDP1Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
3BGC1Ligand/IonBETA-D-GLUCOSE
4GCD1Ligand/Ion4,5-DEHYDRO-D-GLUCURONIC ACID
5GCU1Ligand/IonD-GLUCURONIC ACID
6GLA1Ligand/IonALPHA D-GALACTOSE
7MAN1Ligand/IonALPHA-D-MANNOSE
8MXZ1Ligand/Ion6-DEOXY-2-O-METHYL-ALPHA-L-GALACTOPYRANOSE
9PCA1Mod. Amino AcidPYROGLUTAMIC ACID
10RAM1Ligand/IonALPHA-L-RHAMNOSE
11XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:199 , HIS A:202 , ASP A:233 , SER A:234 , TYR A:257 , GLY A:258 , ASN A:280 , PHE A:282 , LYS A:463 , LYS A:497 , LYS A:501 , HOH A:705 , HOH A:717 , HOH A:739 , HOH A:746 , HOH A:751 , HOH A:754 , HOH A:768 , HOH A:778 , HOH A:789 , HOH A:799 , HOH A:809 , HOH A:836 , HOH A:867 , HOH A:871 , HOH A:879 , HOH A:914 , HOH A:921 , HOH A:946 , HOH A:973 , HOH A:988 , HOH A:1008 , HOH A:1034binding site for Poly-Saccharide residues MAN A 601 through BGC A 607
2AC2SOFTWAREARG A:199 , HIS A:202 , ASP A:233 , SER A:234 , GLU A:245 , TYR A:257 , GLY A:258 , ARG A:271 , ASN A:280 , PHE A:282 , TRP A:298 , ARG A:318 , HIS A:334 , LEU A:360 , ARG A:363 , ARG A:364 , LYS A:463 , LYS A:497 , LYS A:501 , HOH A:705 , HOH A:715 , HOH A:717 , HOH A:719 , HOH A:728 , HOH A:739 , HOH A:746 , HOH A:749 , HOH A:751 , HOH A:754 , HOH A:768 , HOH A:777 , HOH A:778 , HOH A:789 , HOH A:799 , HOH A:809 , HOH A:823 , HOH A:836 , HOH A:840 , HOH A:847 , HOH A:855 , HOH A:867 , HOH A:871 , HOH A:873 , HOH A:879 , HOH A:914 , HOH A:920 , HOH A:921 , HOH A:929 , HOH A:946 , HOH A:973 , HOH A:986 , HOH A:988 , HOH A:997 , HOH A:1008 , HOH A:1010 , HOH A:1034 , HOH A:1096 , HOH A:1105 , HOH A:1132 , HOH A:1147binding site for Poly-Saccharide residues ASG A 608 through GCD A 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OFM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:293 -Gly A:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OFM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OFM)

(-) Exons   (0, 0)

(no "Exon" information available for 1OFM)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:481
 aligned with CSLB_PEDHD | Q46079 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:481
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505 
           CSLB_PEDHD    26 QVVASNETLYQVVKEVKPGGLVQIADGTYKDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRAIQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTDKITFDQVINLNNTARAIKDGSVGGPAMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGRCLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQRFGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFINVNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKNSWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDEVRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH 506
               SCOP domains d1ofma_ A: Chondroitinase B                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -1ofmA00 A:27-506 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhh....eeee..eeee..eeee.........eeeee.....eeeee..eeee....eeee..eeeee..............eee.....eee..eee.........eee............eee..eee........eee...................eee..eeee..........eee..........eee..eeeee....eeeeee....eee..eee....eeeeee....eee..eeee.........eee.....eee..eeee.........eeeee...............eee..eee....eeee...hhhhhhhhhhhhh.........eee..eee.........ee.........eee..eee............hhhhh................hhhhhhhhh......hhhhhh.................hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ofm A  26 xVVASNETLYQVVKEVKPGGLVQIADGTYKDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRAIQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTDKITFDQVINLNNTARAIKDGSVGGPAMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGRCLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQRFGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFINVNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKNSWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDEVRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH 506
                            |       35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505 
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                           26-PCA
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OFM)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CSLB_PEDHD | Q46079)
molecular function
    GO:0033999    chondroitin B lyase activity    Catalysis of the reaction: dermatan sulfate = n 4-deoxy-beta-D-gluc-4-enuronosyl-(1,3)-N-acetyl-D-galactosamine 4-sulfate. This reaction is the eliminative cleavage of dermatan sulfate containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucurosonyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups to yield a 4,5-unsaturated dermatan-sulfate disaccharide (DeltaUA-GalNAC-4S). Chondroitin sulfate B is also known as dermatan sulfate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CSLB_PEDHD | Q46079: 1dbg 1dbo 1ofl

(-) Related Entries Specified in the PDB File

1dbg CRYSTAL STRUCTURE OF CHONDROITINASE B
1dbo CRYSTAL STRUCTURE OF CHONDROITINASE B
1ofl CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO DERMATAN SULFATE HEXASACCHARIDE