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(-) Description

Title :  CRYSTAL STRUCTURE OF PECTATE LYASE FROM BACILLUS SP. STRAIN KSM-P15.
 
Authors :  M. Akita, A. Suzuki, T. Kobayashi, S. Ito, T. Yamane
Date :  31 Jan 00  (Deposition) - 31 Jan 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Parallel Beta-Helix, High-Alkaline, Low-Molecular-Weight, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Akita, A. Suzuki, T. Kobayashi, S. Ito, T. Yamane
The First Structure Of Pectate Lyase Belonging To Polysaccharide Lyase Family 3.
Acta Crystallogr. , Sect. D V. 57 1786 2001
PubMed-ID: 11717490  |  Reference-DOI: 10.1107/S0907444900003334

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A
    EC Number: 4.2.2.2
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 98226
    Strain: KSM-P15

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:80 , VAL A:81 , LYS A:103 , HOH A:327 , HOH A:359 , HOH A:467BINDING SITE FOR RESIDUE CA A 300

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:67 -A:71

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:59 -Pro A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EE6)

(-) Exons   (0, 0)

(no "Exon" information available for 1EE6)

(-) 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:197
 aligned with Q9RHW0_BACSP | Q9RHW0 from UniProtKB/TrEMBL  Length:224

    Alignment length:197
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       
         Q9RHW0_BACSP    28 APTVVHETIRVPAGQTFDGKGQTYVANPNTLGDGSQAENQKPIFRLEAGASLKNVVIGAPAADGVHCYGDCTITNVIWEDVGEDALTLKSSGTVNISGGAAYKAYDKVFQINAAGTINIRNFRADDIGKLVRQNGGTTYKVVMNVENCNISRVKDAILRTDSSTSTGRIVNTRYSNVPTLFKGFKSGNTTASGNTQY 224
               SCOP domains d1ee6a_ A: Pectate lyase                                                                                                                                                                              SCOP domains
               CATH domains 1ee6A00 A:1-197 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee....eeeeeeeeeee.................eee...eeeeeeee.......eeee..eeeeeeee.......eeeee.eeeeee..eeeeeeeeeeee...eeeeee..eeeeeeeeeee.......eeeeee..eeeeeeeeeee......eeeee..eee.....ee......eeee..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ee6 A   1 APTVVHETIRVPAGQTFDGKGQTYVANPNTLGDGSQAENQKPIFRLEAGASLKNVVIGAPAADGVHCYGDCTITNVIWEDVGEDALTLKSSGTVNISGGAAYKAYDKVFQINAAGTINIRNFRADDIGKLVRQNGGTTYKVVMNVENCNISRVKDAILRTDSSTSTGRIVNTRYSNVPTLFKGFKSGNTTASGNTQY 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1EE6)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9RHW0_BACSP | Q9RHW0)
molecular function
    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.
    GO:0030570    pectate lyase activity    Catalysis of the reaction: a pectate = a pectate + a pectate oligosaccharide with 4-(4-deoxy-alpha-D-galact-4-enuronosyl)-D-galacturonate end. This reaction is the eliminative cleavage of pectate to give oligosaccharides with 4-deoxy-alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
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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