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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MARINE PL7 ALGINATE LYASE ALYA1 FROM ZOBELLIA GALACTANIVORANS
 
Authors :  F. Thomas, A. Jeudy, G. Michel, M. Czjzek
Date :  04 Mar 13  (Deposition) - 26 Jun 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lyase, Polysaccharidases, Marine Bacterial Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Thomas, L. C. E. Lundqvist, M. Jam, A. Jeudy, T. Barbeyron, C. Sandstrom, G. Michel, M. Czjzek
Comparative Characterization Of Two Marine Alginate Lyases From Zobellia Galactanivorans Reveals Distinct Modes Of Action And Exquisite Adaptation To Their Natural Substrate.
J. Biol. Chem. V. 288 23021 2013
PubMed-ID: 23782694  |  Reference-DOI: 10.1074/JBC.M113.467217

(-) Compounds

Molecule 1 - ALGINATE LYASE, FAMILY PL7
    Chains: A, B
    EC Number: 4.2.2.3, 4.2.2.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PFO4
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 199-446
    Organism Scientific: ZOBELLIA GALACTANIVORANS
    Organism Taxid: 63186
    Other Details: INHOUSE ISOLATE OF ROSCOFF MARINE INSTITUTE AND DSM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:233 , ALA A:235 , ILE A:238 , SER A:352 , HOH A:2344BINDING SITE FOR RESIDUE NA A 450
2AC2SOFTWARETHR B:233 , ASP B:234 , LYS B:354 , SER B:372 , HOH B:2049BINDING SITE FOR RESIDUE NA B 450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZPY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZPY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZPY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZPY)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZPY)

(-) Sequences/Alignments

Asymmetric 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:248
 aligned with G0LAE1_ZOBGA | G0LAE1 from UniProtKB/TrEMBL  Length:446

    Alignment length:248
                                   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438        
         G0LAE1_ZOBGA   199 GNSPASVLGITANTWKINSFIGSPGSSATYYDDITDASGISYNTYSDDNYFYTDGEWVYFKCYRGLGGSANSQNPRVELREMDNGNLASWTGDSGTHTMEWTVQVNQLPQDTDGDGGVLCFGQIHGPSKNSDGVEVDDVVRVQFIGEENQSSGSVKLKISGYVTEEQGGSQTFSGYSLDTTYNCKLVYSGGYVELFMNGSSVFRKKMEVDDLSENYFKVGNYLQSVKGASYTGSYGLVRIKNLSVTHN 446
               SCOP domains d3zpya_ A: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.....eeeeeee.......eee.hhhhh...hhhhh.....eee....eeeeee............eeeeeeee..ee........eeeeeeeeeeee.........eeeeeeeee............eeeeeeeee.......eeeeeeehhhhhh....eeeeeee....eeeeeeee..eeeeee..eeeeeee.........eeeeeeee...........eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpy A 199 GNSPASVLGITANTWKINSFIGSPGSSATYYDDITDASGISYNTYSDDNYFYTDGEWVYFKCYRGLGGSANSQNPRVELREMDNGNLASWTGDSGTHTMEWTVQVNQLPQDTDGDGGVLCFGQIHGPSKNSDGVEVDDVVRVQFIGEENQSSGSVKLKISGYVTEEQGGSQTFSGYSLDTTYNCKLVYSGGYVELFMNGSSVFRKKMEVDDLSENYFKVGNYLQSVKGASYTGSYGLVRIKNLSVTHN 446
                                   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438        


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with G0LAE1_ZOBGA | G0LAE1 from UniProtKB/TrEMBL  Length:446

    Alignment length:247
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       
         G0LAE1_ZOBGA   200 NSPASVLGITANTWKINSFIGSPGSSATYYDDITDASGISYNTYSDDNYFYTDGEWVYFKCYRGLGGSANSQNPRVELREMDNGNLASWTGDSGTHTMEWTVQVNQLPQDTDGDGGVLCFGQIHGPSKNSDGVEVDDVVRVQFIGEENQSSGSVKLKISGYVTEEQGGSQTFSGYSLDTTYNCKLVYSGGYVELFMNGSSVFRKKMEVDDLSENYFKVGNYLQSVKGASYTGSYGLVRIKNLSVTHN 446
               SCOP domains d3zpyb_ B: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.....eeeeeee.......eee.hhhhh.............eee....eeeeee............eeeeeeee..ee........eeeeeeeeeeee.........eeeeeeeee............eeeeeeeee.......eeeeeeehhhhhh....eeeeeee....eeeeeeee..eeeeee..eeeeeee.........eeeeeeee...........eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zpy B 200 NSPASVLGITANTWKINSFIGSPGSSATYYDDITDASGISYNTYSDDNYFYTDGEWVYFKCYRGLGGSANSQNPRVELREMDNGNLASWTGDSGTHTMEWTVQVNQLPQDTDGDGGVLCFGQIHGPSKNSDGVEVDDVVRVQFIGEENQSSGSVKLKISGYVTEEQGGSQTFSGYSLDTTYNCKLVYSGGYVELFMNGSSVFRKKMEVDDLSENYFKVGNYLQSVKGASYTGSYGLVRIKNLSVTHN 446
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZPY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZPY)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (G0LAE1_ZOBGA | G0LAE1)
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:0045135    poly(beta-D-mannuronate) lyase activity    Catalysis of the reaction: polysaccharides containing beta-D-mannuronate residues = oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enopyranuronosyl end. This reaction is the eliminative cleavage of polysaccharides containing beta-D-mannuronate residues to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enopyranuronosyl groups at their ends.

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4be3 CRYSTAL STRUCTURE OF THE EXOLYTIC PL7 ALGINATE LYASE ALYA5 FROM ZOBELLIA GALACTANIVORANS