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(-) Description

Title :  CRYSTAL STRUCTURE OF PECTATE LYASE C R218K MUTANT IN COMPLEX WITH PENTAGALACTURONIC ACID
 
Authors :  R. D. Scavetta, F. Jurnak
Date :  02 Nov 05  (Deposition) - 15 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Parallel Beta Helix, Protein-Oligosaccharide Interactions, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. D. Scavetta, S. R. Herron, A. T. Hotchkiss, N. Kita, N. T. Keen, J. A. Benen, H. C. Kester, J. Visser, F. Jurnak
Structure Of A Plant Cell Wall Fragment Complexed To Pectate Lyase C
Plant Cell V. 11 1081 1999
PubMed-ID: 10368179  |  Reference-DOI: 10.1105/TPC.11.6.1081
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTATE LYASE C
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET5A
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PELC
    Mutation: YES
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556
    Strain: EC16

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ADA4Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA4Ligand/IonCALCIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:216 , TYR A:268 , CA A:704 , ADA A:902 , HOH A:1047 , HOH A:1048BINDING SITE FOR RESIDUE ADA A 901
2AC2SOFTWAREASP A:160 , ASP A:162 , LYS A:218 , LEU A:221 , ARG A:245 , TYR A:268 , CA A:703 , CA A:704 , ADA A:901 , ADA A:903 , HOH A:1046 , HOH A:1061BINDING SITE FOR RESIDUE ADA A 902
3AC3SOFTWAREASP A:162 , LYS A:190 , LEU A:193 , SER A:196 , ARG A:223 , CA A:702 , CA A:703 , ADA A:902 , ADA A:904 , HOH A:1076 , HOH A:1077 , HOH A:1078 , HOH A:1203BINDING SITE FOR RESIDUE ADA A 903
4AC4SOFTWAREASP A:129 , GLU A:166 , ASP A:170 , LYS A:172 , LEU A:193 , SER A:308 , CA A:701 , CA A:702 , ADA A:903 , HOH A:1073 , HOH A:1074 , HOH A:1078 , HOH A:1079 , HOH A:1082 , HOH A:1203 , HOH A:1204BINDING SITE FOR RESIDUE ADA A 904
5AC5SOFTWAREASP A:129 , ASP A:131 , GLU A:166 , ASP A:170 , ADA A:904 , HOH A:1204BINDING SITE FOR RESIDUE CA A 701
6AC6SOFTWAREGLU A:166 , ADA A:903 , ADA A:904 , HOH A:1074 , HOH A:1076 , HOH A:1203BINDING SITE FOR RESIDUE CA A 702
7AC7SOFTWAREASP A:160 , ASP A:162 , ADA A:902 , ADA A:903 , HOH A:1077 , HOH A:1078BINDING SITE FOR RESIDUE CA A 703
8AC8SOFTWARELYS A:218 , TYR A:268 , ADA A:901 , ADA A:902 , HOH A:1308BINDING SITE FOR RESIDUE CA A 704

(-) 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 2EWE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EWE)

(-) Exons   (0, 0)

(no "Exon" information available for 2EWE)

(-) 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:352
 aligned with PLYC_DICCH | P11073 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:352
                                    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 ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKGGAYPLVITYTGNEDSLINAAAANICGQWSKDPRGVEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNARLPLQRGGLVHAYNNLYTNITGSGLNVRQNGQALIENNWFEKAINPVTSRYDGKNFGTWVLKGNNITKPADFSTYSITWTADTKPYVNADSWTSTGTFPTVAYNYSPVSAQCVKDKLPGYAGVGKNLATLTSTAC 374
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2eweA00 A:1-352 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.......eee....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
                 2ewe A   1 ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKGGAYPLVITYTGNEDSLINAAAANICGQWSKDPRGVEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNAKLPLQRGGLVHAYNNLYTNITGSGLNVRQNGQALIENNWFEKAINPVTSRYDGKNFGTWVLKGNNITKPADFSTYSITWTADTKPYVNADSWTSTGTFPTVAYNYSPVSAQCVKDKLPGYAGVGKNLATLTSTAC 352
                                    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)
  - → 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  (0, 0)

(no "SCOP Domain" information available for 2EWE)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EWE)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        PLYC_DICCH | P11073: 1air 1o88 1o8d 1o8e 1o8f 1o8g 1o8h 1o8i 1o8j 1o8k 1o8l 1o8m 1plu 2pec

(-) Related Entries Specified in the PDB File

1air PELC (WILD-TYPE), UNCOMPLEXED
1plu PELC (WILD-TYPE), WITH LU+3 IN THE PUTATIVE CA+2 BINDING SITE.