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(-) Description

Title :  CHONDROITINASE AC LYASE FROM FLAVOBACTERIUM HEPARINUM
 
Authors :  J. Fethiere, B. Eggimann, M. Cygler
Date :  02 Mar 99  (Deposition) - 14 May 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Chondroitin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Fethiere, B. Eggimann, M. Cygler
Crystal Structure Of Chondroitin Ac Lyase, A Representative Of A Family Of Glycosaminoglycan Degrading Enzymes.
J. Mol. Biol. V. 288 635 1999
PubMed-ID: 10329169  |  Reference-DOI: 10.1006/JMBI.1999.2698
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CHONDROITINASE AC)
    Cellular Location: INTRACELLULAR
    Chains: A
    EC Number: 4.2.2.5
    Organism Scientific: PEDOBACTER HEPARINUS
    Organism Taxid: 984

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 7)

Asymmetric/Biological Unit (7, 7)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GCU1Ligand/IonD-GLUCURONIC ACID
3GOL1Ligand/IonGLYCEROL
4MAN1Ligand/IonALPHA-D-MANNOSE
5MFU1Ligand/IonALPHA-L-METHYL-FUCOSE
6RAM1Ligand/IonALPHA-L-RHAMNOSE
7XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:455 , ASN A:479 , RAM A:2001 , GCU A:2002BINDING SITE FOR RESIDUE MAN A 2000
2AC2SOFTWAREASN A:479 , MAN A:2000BINDING SITE FOR RESIDUE RAM A 2001
3AC3SOFTWAREARG A:415 , ARG A:421 , MAN A:2000 , XYP A:2003 , HOH A:3181BINDING SITE FOR RESIDUE GCU A 2002
4AC4SOFTWAREGCU A:2002BINDING SITE FOR RESIDUE XYP A 2003
5AC5SOFTWAREGLU A:405 , ASP A:407 , ASP A:416 , TYR A:417 , HOH A:3200 , HOH A:3202BINDING SITE FOR RESIDUE CA A 3000
6AC6SOFTWARESER A:233 , TYR A:234 , GLU A:286 , ARG A:288 , GLY A:289 , ARG A:292 , HOH A:3092 , HOH A:3265BINDING SITE FOR RESIDUE GOL A 2010
7ACTAUTHORHIS A:225 , ARG A:288 , ARG A:292HYPOTHETICAL ACTIVE SITE WITH THE HIS SERVING AS THE CATALYTIC BASE
8CALAUTHORGLU A:405 , ASP A:407 , TYR A:417 , ASP A:416 , HOH A:3312 , HOH A:3313CALCIUM BINDING SITE IN THE BETA-SHEET DOMAIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CB8)

(-) Exons   (0, 0)

(no "Exon" information available for 1CB8)

(-) 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:675
 aligned with CSLA_PEDHD | Q59288 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:675
                                    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       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695     
           CSLA_PEDHD    26 GTAELIMKRVMLDLKKPLRNMDKVAEKNLNTLQPDGSWKDVPYKDDAMTNWLPNNHLLQLETIIQAYIEKDSHYYGDDKVFDQISKAFKYWYDSDPKSRNWWHNEIATPQALGEMLILMRYGKKPLDEALVHKLTERMKRGEPEKKTGANKTDIALHYFYRALLTSDEALLSFAVKELFYPVQFVHYEEGLQYDYSYLQHGPQLQISSYGAVFITGVLKLANYVRDTPYALSTEKLAIFSKYYRDSYLKAIRGSYMDFNVEGRGVSRPDILNKKAEKKRLLVAKMIDLKHTEEWADAIARTDSTVAAGYKIEPYHHQFWNGDYVQHLRPAYSFNVRMVSKRTRRSESGNKENLLGRYLSDGATNIQLRGPEYYNIMPVWEWDKIPGITSRDYLTDRPLTKLWGEQGSNDFAGGVSDGVYGASAYALDYDSLQAKKAWFFFDKEIVCLGAGINSNAPENITTTLNQSWLNGPVISTAGKTGRGKITTFKAQGQFWLLHDAIGYYFPEGANLSLSTQSQKGNWFHINNSHSKDEVSGDVFKLWINHGARPENAQYAYIVLPGINKPEEIKKYNGTAPKVLANTNQLQAVYHQQLDMVQAIFYTAGKLSVAGIEIETDKPCAVLIKHINGKQVIWAADPLQKEKTAVLSIRDLKTGKTNRVKIDFPQQEFAGATVELK 700
               SCOP domains d1cb8a1 A:26-335 Chondroitinase AC                                                                                                                                                                                                                                                                                    d1cb8a3 A:336-599 Chondroitinase AC                                                                                                                                                                                                                                     d1cb8a2 A:600-700 Chondroitinase AC                                                                   SCOP domains
               CATH domains -1cb8A01 A:27-338  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                   -----1cb8A02 A:344-589  [code=2.70.98.10, no name defined]                                                                                                                                                                                                 1cb8A03 A:590-699 Chondroitinase Ac; Chain A, domain 3                                                        - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......hhhhhhhhhhh....................hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhh....hhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..hhh.......hhh.hhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhh............eeeee....eeeee....eeeee.........................eeeee...hhh...hhh.........eee....................eeeee....eeeeeeeee..eeeeeeeee....eeeeee........eeeee.eeee....eee..eee....eeeeee...eeeee..eeeee...eeeeee..eeeee...........eeeeeeeeeeeeeee......eeeeeee....hhhhh..hhh..eeeee...eeeeee....eeeeee...eeeee..eeeee...eeeeee......eeeee.......eeeeeeee.....eeeeeee...hhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cb8 A  26 GTAELIMKRVMLDLKKPLRNMDKVAEKNLNTLQPDGSWKDVPYKDDAMTNWLPNNHLLQLETIIQAYIEKDSHYYGDDKVFDQISKAFKYWYDSDPKSRNWWHNEIATPQALGEMLILMRYGKKPLDEALVHKLTERMKRGEPEKKTGANKTDIALHYFYRALLTSDEALLSFAVKELFYPVQFVHYEEGLQYDYSYLQHGPQLQISSYGAVFITGVLKLANYVRDTPYALSTEKLAIFSKYYRDSYLKAIRGSYMDFNVEGRGVSRPDILNKKAEKKRLLVAKMIDLKHTEEWADAIARTDSTVAAGYKIEPYHHQFWNGDYVQHLRPAYSFNVRMVSKRTRRSESGNKENLLGRYLSDGATNIQLRGPEYYNIMPVWEWDKIPGITSRDYLTDRPLTKLWGEQGSNDFAGGVSDGVYGASAYALDYDSLQAKKAWFFFDKEIVCLGAGINSNAPENITTTLNQSWLNGPVISTAGKTGRGKITTFKAQGQFWLLHDAIGYYFPEGANLSLSTQSQKGNWFHINNSHSKDEVSGDVFKLWINHGARPENAQYAYIVLPGINKPEEIKKYNGTAPKVLANTNQLQAVYHQQLDMVQAIFYTAGKLSVAGIEIETDKPCAVLIKHINGKQVIWAADPLQKEKTAVLSIRDLKTGKTNRVKIDFPQQEFAGATVELK 700
                                    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       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CB8)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CSLA_PEDHD | Q59288)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0016837    carbon-oxygen lyase activity, acting on polysaccharides    Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0030341    chondroitin AC lyase activity    Catalysis of the eliminative degradation of polysaccharides containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucuronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CSLA_PEDHD | Q59288: 1hm2 1hm3 1hmu 1hmw

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