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(-) Description

Title :  CRYSTAL STRUCTURE OF PECTATE LYASE PEL9A
 
Authors :  J. Jenkins, V. E. Shevchik, N. Hugouvieux-Cotte-Pattat, R. W. Pickersgill
Date :  11 Dec 03  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Parallel Beta-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jenkins, V. E. Shevchik, N. Hugouvieux-Cotte-Pattat, R. W. Pickersgill
The Crystal Structure Of Pectate Lyase Pel9A From Erwinia Chrysanthemi
J. Biol. Chem. V. 279 9139 2004
PubMed-ID: 14670977  |  Reference-DOI: 10.1074/JBC.M311390200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PELL
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556
    Synonym: PEL9A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:209 , ASP A:233 , ASP A:234 , ASP A:237 , HOH A:459 , HOH A:573BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWAREASN A:402 , SER A:413 , ALA A:416 , ASP A:418 , GLU A:423 , HOH A:482BINDING SITE FOR RESIDUE CA A 2

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:114

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RU4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RU4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RU4)

(-) Exons   (0, 0)

(no "Exon" information available for 1RU4)

(-) 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:400
 aligned with PLYL_DICCH | P0C1A6 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:400
                                    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
           PLYL_DICCH    26 ADCSSDLTSGISTKRIYYVAPNGSSSNNGNSFNSPMSFTAAMAAANPGELILLKPGTYTIPYTQGKGNTITFNKSGKEGSPIYVAAANCGRAVFDFSFPDSQWVQASYGFYVTGDYWYFKGIEVTRAGYQGAYVTGSHNTFENTAFHHNRNTGLEINNGGSYNTVINSDAYRNYDPKKNGSMADGFGPKQKQGQGNRFGGCRAWENSDDGFDLFDSPQKVVIENSWAFRNGINYWSDSSFAGNGNGFKLGGNQAVGNHRITRSVAFGNVSKGFDQNNNAGGVTVINNTSYKNGINYGFGSNVKSGQKHYFRNNVSLSGSATVNNADAKSNSWDTGPVASASDFVSLDTSLATISRDNDGTLPETALFRLSTNSKLINAGTKESNISYSGSAPDLGAFERN 425
               SCOP domains d1ru4a_ A: Pectate transeliminase                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1ru4A00 A:26-425 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee.................hhhhhhhhh....eeee..eeee..........eee.........eeeee.hhh.eeee..............eee....eeee.eeee......eee.....eee..eee......eee.......eee..eee..............eee........eee..eee......ee........eee..eee..................ee..........eee..eee....eeee........eee..eee...eeeee.........eeee..eee...eee..eeee..........hhhhh...hhhhhhh............................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ru4 A  26 ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTIPYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFDFSFPDSQWVQASYGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHNRNTGLEINNGGSYNTVINSDAYRNYDPKKNGSMADGFGPKQKQGPGNRFVGCRAWENSDDGFDLFDSPQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQAVGNHRITRSVAFGNVSKGFDQNNNAGGVTVINNTSYKNGINYGFGSNVQSGQKHYFRNNVSLSASVTVSNADAKSNSWDTGPAASASDFVSLDTSLATVSRDNDGTLPETSLFRLSANSKLINAGTKESNISYSGSAPDLGAFERN 425
                                    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


Chain A from PDB  Type:PROTEIN  Length:400
 aligned with PLYL_DICD3 | P0C1A7 from UniProtKB/Swiss-Prot  Length:425

    Alignment length:400
                                    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
           PLYL_DICD3    26 ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTIPYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFDFSFPDSQWVQASYGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHNRNTGLEINNGGSYNTVINSDAYRNYDPKKNGSMADGFGPKQKQGPGNRFVGCRAWENSDDGFDLFDSPQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQAVGNHRITRSVAFGNVSKGFDQNNNAGGVTVINNTSYKNGINYGFGSNVQSGQKHYFRNNVSLSASVTVSNADAKSNSWDTGPAASASDFVSLDTSLATVSRDNDGTLPETSLFRLSANSKLINAGTKESNISYSGSAPDLGAFERN 425
               SCOP domains d1ru4a_ A: Pectate transeliminase                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1ru4A00 A:26-425 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeee.................hhhhhhhhh....eeee..eeee..........eee.........eeeee.hhh.eeee..............eee....eeee.eeee......eee.....eee..eee......eee.......eee..eee..............eee........eee..eee......ee........eee..eee..................ee..........eee..eee....eeee........eee..eee...eeeee.........eeee..eee...eee..eeee..........hhhhh...hhhhhhh............................................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ru4 A  26 ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTIPYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFDFSFPDSQWVQASYGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHNRNTGLEINNGGSYNTVINSDAYRNYDPKKNGSMADGFGPKQKQGPGNRFVGCRAWENSDDGFDLFDSPQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQAVGNHRITRSVAFGNVSKGFDQNNNAGGVTVINNTSYKNGINYGFGSNVQSGQKHYFRNNVSLSASVTVSNADAKSNSWDTGPAASASDFVSLDTSLATVSRDNDGTLPETSLFRLSANSKLINAGTKESNISYSGSAPDLGAFERN 425
                                    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
   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 1RU4)

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLYL_DICD3 | P0C1A7)
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.

Chain A   (PLYL_DICCH | P0C1A6)
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: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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