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(-) Description

Title :  CRYSTAL STRUCTURE OF FAMILY 7 ALGINATE LYASE A1-II' Y284F IN CMPLEX WITH PRODUCT (GGG)
 
Authors :  K. Ogura, M. Yamasaki, B. Mikami, W. Hashimoto, K. Murata
Date :  02 Oct 07  (Deposition) - 27 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A
Keywords :  Alginate Lyase, Polysaccharide Lyase Family 7, Y284F, Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ogura, M. Yamasaki, B. Mikami, W. Hashimoto, K. Murata
Substrate Recognition In Tunnel Of Family 7 Alginate Lyase From Sphingomonas Sp. A1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALGINATE LYASE
    Chains: A
    EC Number: 4.2.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 81-313
    Gene: ALY
    Mutation: YES
    Organism Scientific: SPHINGOMONAS SP.
    Organism Taxid: 90322
    Strain: A1
    Synonym: ALGINATE LYASE A1-II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1BEM1Ligand/IonBETA-D-MANNURONIC ACID
2GOL1Ligand/IonGLYCEROL
3LGU3Ligand/IonALPHA-L-GULURONATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:95 , GLN A:97 , GLU A:105 , ARG A:150 , HOH A:606 , HOH A:638 , HOH A:696 , HOH A:714 , HOH A:779 , HOH A:788BINDING SITE FOR RESIDUE LGU A 401
2AC2SOFTWAREGLN A:97 , THR A:139 , ALA A:140 , ASN A:141 , SER A:142 , ARG A:146 , HIS A:191 , ASN A:199 , TYR A:278 , LYS A:280 , HOH A:696 , HOH A:753BINDING SITE FOR RESIDUE LGU A 402
3AC3SOFTWAREASN A:141 , ARG A:146 , GLN A:189 , HIS A:191 , ASN A:199 , ALA A:200 , PRO A:202 , PHE A:284 , HOH A:663 , HOH A:668 , HOH A:753BINDING SITE FOR RESIDUE LGU A 403
4AC4SOFTWAREASN A:141 , ARG A:146 , GLN A:189 , HIS A:191 , ASN A:199 , PHE A:284 , HOH A:663 , HOH A:753BINDING SITE FOR RESIDUE BEM A 501
5AC5SOFTWAREASN A:88 , GLY A:126 , TYR A:144 , ASN A:288 , TYR A:300 , HOH A:686BINDING SITE FOR RESIDUE GOL A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZAB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZAB)

(-) 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:226
 aligned with Q75WP3_9SPHN | Q75WP3 from UniProtKB/TrEMBL  Length:308

    Alignment length:226
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301      
         Q75WP3_9SPHN    82 AAAPGKNFDLSHWKLQLPDANTTEISSANLGLGYTSQYFYTDTDGAMTFWAPTTGGTTANSSYPRSELREMLDPSNSKVNWGWQGTHTMKLSGKTVQLPSSGKIIVAQIHGIMDDGTNAPPLVKAVFQDGQLDMQVKQNSDGTGSDVHNYFTGIKLGDLYNMEIRVTDGVAYVTMNGDTRSVDFVGKDAGWKNLKYYFKAGNYVQDNTSTGGSAIAKLYSLSVSHS 307
               SCOP domains d2zaba_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------Alginate_lyase2-2zabA01 A:89-306                                                                                                                                                                                          - Pfam domains
         Sec.struct. author ..hhhhhh....eeee.......eehhhhhhh......eee.....eeeeee............eeeeee...............eeeeeeeeeeee......eeeeeeeee.....eeeeeeeeeee..eeeeeee........ee..eee.......eeeeeeee..eeeeee..eeeeeehhhhhhhhhhheeeeeeeeee........eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zab A  82 AAAPGKNFDLSHWKLQLPDANTTEISSANLGLGYTSQYFYTDTDGAMTFWAPTTGGTTANSSYPRSELREMLDPSNSKVNWGWQGTHTMKLSGKTVQLPSSGKIIVAQIHGIMDDGTNAPPLVKAVFQDGQLDMQVKQNSDGTGSDVHNYFTGIKLGDLYNMEIRVTDGVAYVTMNGDTRSVDFVGKDAGWKNLKYYFKAGNFVQDNTSTGGSAIAKLYSLSVSHS 307
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Alginate_lyase2] (7)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q75WP3_9SPHN | Q75WP3)
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q75WP3_9SPHN | Q75WP3: 2cws 2z42 2za9 2zaa 2zac

(-) Related Entries Specified in the PDB File

2cws THE LINGAD-FREE WILD-TYPE PROTEIN
2z42 THE LINGAD-FREE WILD-TYPE PROTEIN
2za9
2zaa
2zac