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(-) Description

Title :  STRUCTURE OF A FAMILY 2 PECTATE LYASE IN COMPLEX WITH TRIGALACTURONIC ACID
 
Authors :  D. W. Abbott, A. B. Boraston
Date :  08 Aug 07  (Deposition) - 18 Sep 07  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, 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 Beta-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  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ADA2Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:132 , ARG A:171 , PHE A:201 , ASN A:203 , TYR A:248 , ARG A:272 , ARG A:295 , TYR A:364 , GLU A:515 , ARG A:530 , HOH A:2175 , HOH A:2586 , HOH A:2587 , HOH A:2588 , HOH A:2589BINDING SITE FOR POLY-SACCHARIDE RESIDUES ADA A1547 THROUGH ADA A1549

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V8K)

(-) 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 2V8K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V8K)

(-) Exons   (0, 0)

(no "Exon" information available for 2V8K)

(-) 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:543
 aligned with A1JSS8_YERE8 | A1JSS8 from UniProtKB/TrEMBL  Length:572

    Alignment length:543
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566   
         A1JSS8_YERE8    27 DRLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPSEKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKTGLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDGYYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVDAIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNVGEKLQPN 569
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Pectate_lyase_2-2v8kA01 A:4-546                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...............ee........eee.....eeeeehhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............eee.....ee................hhhhhhhhhhhhhhhhhhhhhhhheee....ee...........hhhhh........eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eee............hhhhhhhhhhhhhhhhh...hhh.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....ee..ee........ee............ee..ee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..ee.........ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee..ee........ee...hhhhhhhhhhhhhh.hhhhh..........eeeee.....eeeeeehhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8k A   4 DRLTVVKQYVDNVLNKASDTYHGDKPSPLLADGVDPRTGQQLEWIFPDGRRAVLSNFSAQQNLMRVMSGLSQLSGDPRYQKRAEDIVRYHFQNYQDPSGLLYWGGHRFVDLKTLQPEGPSEKEMVHELKNAYPYYDLMFSVDSDATARFIRGFWNAHVYDWRILETSRHGEYGKPMGALWESKFEQQPPFFATKGLSFLNAGNDLIYSASLLYKHQQDQGALTWAKRLADQYVLPRDAKTGLGVYQFTQALKREEPTDDADTHSKFGDRAQRQFGPEFGPTALEGNMMLKGRTSTLYSENALMQLQLGKDLGPQGQDLLKWTVDGLKAFAKYAYNDQDNTFRPMIANGQDLSNYTLPRDGYYGKKGTVLKPYKAGNEFLISYARAYAIDNDPLLWKVARGIANDQGLGDIGTAPGKEVKVNMDTTNSDPYALFALLDLYHASQVADYRKLAEKIGDNIIKIRYIDGFFMASSDRQYADVDAIEPYALLALEASLRNKPQAVAPFLNGAGFTEGAYRMDDGSARVSTRDNELFLLNVGEKLQPN 546
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543
   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 2V8K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V8K)

(-) 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 2v8j

(-) Related Entries Specified in the PDB File

2v8i STRUCTURE OF A FAMILY 2 PECTATE LYASE IN A NATIVE FORM
2v8j STRUCTURE OF A FAMILY 2 PECTATE LYASE IN COMPLEX WITH A TRANSITION METAL