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(-) Description

Title :  PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 5MM CA2+
 
Authors :  S. R. Herron, F. A. Jurnak
Date :  27 Nov 02  (Deposition) - 30 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Pectate Lyase Cleavage, Calcium Binding, Parallel Beta- Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Herron, R. Scavetta, M. Garrett, M. Legner, F. A. Jurnak
Characterization And Implications Of Ca2+ Binding To Pectate Lyase C
J. Biol. Chem. V. 278 12271 2003
PubMed-ID: 12540845  |  Reference-DOI: 10.1074/JBC.M209306200

(-) Compounds

Molecule 1 - PECTATE LYASE C
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556

 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:129 , ASP A:131 , GLU A:166 , ASP A:170 , HOH A:2066 , HOH A:2079BINDING SITE FOR RESIDUE CA A1353

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:72 -A:155
2A:329 -A:352

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:219 -Pro A:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O8G)

(-) Exons   (0, 0)

(no "Exon" information available for 1O8G)

(-) 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:353
 aligned with PLYC_DICCH | P11073 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:353
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372   
           PLYC_DICCH    23 ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKGGAYPLVITYTGNEDSLINAAAANICGQWSKDPRGVEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNARLPLQRGGLVHAYNNLYTNITGSGLNVRQNGQALIENNWFEKAINPVTSRYDGKNFGTWVLKGNNITKPADFSTYSITWTADTKPYVNADSWTSTGTFPTVAYNYSPVSAQCVKDKLPGYAGVGKNLATLTSTACK 375
               SCOP domains d1o8ga_ A: Pectate lyase                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1o8gA00 A:1-353 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.hhhhhhhhhhhh...............eeeee...hhhhhhhhhhhhhhh......eeeee.....eeeee........eeeee....eeee..eee...hhhhh...eeee....eeee..eee........hhhhh......eeee....eeeee..eeeeeee..ee.........eeeee..eeeeeee...eee..eeeee..eeeee....eeee...eeeee..eeeeee..eee........eeeee.......hhhhhh.ee........ee....................hhhhhhhhhhhh..........hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o8g A   1 ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKGGAYPLVITYTGNEDSLINAAAANICGQWSKDPRGVEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNARLPLQRGGLVHAYNNLYTNITGSGLNVRQNGQALIENNWFEKAINPVTSRYDGKNFGTWVLKGNNITKPADFSTYSITWTADTKPYVNADSWTSTGTFPTVAYNYSPVSAQCVKDKLPGYAGVGKNLATLTSTACK 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350
   Legend:   → Mismatch (orange background)
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  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 1O8G)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLYC_DICCH | P11073)
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.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0045490    pectin catabolic process    The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.
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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  1o8g
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  4.2.2.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        PLYC_DICCH | P11073: 1air 1o88 1o8d 1o8e 1o8f 1o8h 1o8i 1o8j 1o8k 1o8l 1o8m 1plu 2ewe 2pec

(-) Related Entries Specified in the PDB File

1air PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI ( EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS
1o88 PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 11.2 WITH 30MM CA2+
1o8d PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 11.2 WITH 5MM CA2+
1o8e PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 11.2 WITH 1MM CA2+
1o8f PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 30MM CA2+
1o8h PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 0.3MM CA2+ ADDED
1o8i PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH NO CA2+ ADDED
1o8j PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH 30MM CA2+
1o8k PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH 20MM CA2+
1o8l PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH 5MM CA2+
1o8m PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 4.5 WITH NO CA2+ ADDED
1plu PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE
2pec PECTATE LYASE C (PLC)