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(-) Description

Title :  STRUCTURE OF A FAMILY 2 PECTATE LYASE IN COMPLEX WITH A TRANSITION METAL
 
Authors :  D. W. Abbott, A. B. Boraston
Date :  08 Aug 07  (Deposition) - 18 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Periplasm, Pectate Lyase, Beta-Elimination, Pectin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Abbott, A. B. Boraston
A Family 2 Pectate Lyase Displays A Rare Fold And Transition Metal-Assisted -Elimination.
J. Biol. Chem. V. 282 35328 2007
PubMed-ID: 17881361  |  Reference-DOI: 10.1074/JBC.M705511200

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630

 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
1MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:109 , GLU A:130 , HIS A:172 , HOH A:2344 , HOH A:2345 , HOH A:2346BINDING SITE FOR RESIDUE MN A1540

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V8J)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:246 -Val A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V8J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V8J)

(-) Exons   (0, 0)

(no "Exon" information available for 2V8J)

(-) 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:535
 aligned with A1JSS8_YERE8 | A1JSS8 from UniProtKB/TrEMBL  Length:572

    Alignment length:535
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557     
         A1JSS8_YERE8    28 RLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPSEKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKTGLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDGYYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVDAIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNV 562
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Pectate_lyase_2-2v8jA01 A:5-539                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...............ee........eee.....eeeeehhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............eee.....ee................hhhhhhhhhhhhhhhhhhhhhhhheee....ee...........hhhhh........eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eee............hhhhhhhhhhhhhhhhh...hhh.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....ee..ee...ee...ee............ee..ee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..ee.........ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee........ee...hhhhhhhhhhhhhh................eeeee.....eeeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8j A   5 RLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPSEKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKTGLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDGYYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVDAIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNV 539
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534
   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 2V8J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V8J)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Pectate_lyase_2] (3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A1JSS8_YERE8 | A1JSS8)
molecular function
    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: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: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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/TrEMBL
        A1JSS8_YERE8 | A1JSS8: 2v8i 2v8k

(-) Related Entries Specified in the PDB File

2v8i STRUCTURE OF A FAMILY 2 PECTATE LYASE IN A NATIVE FORM
2v8k STRUCTURE OF A FAMILY 2 PECTATE LYASE IN COMPLEX WITH TRIGALACTURONIC ACID