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(-) Description

Title :  CRYSTAL STRUCTURE OF FAMILY 7 ALGINATE LYASE A1-II' H191N/Y284F IN COMPLEX WITH SUBSTRATE (GGMG)
 
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 :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Alginate Lyase, Polysaccharide Lyase Family 7, Y284F_tetrasacchride 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  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1BEM1Ligand/IonBETA-D-MANNURONIC ACID
2GOL1Ligand/IonGLYCEROL
3LGU3Ligand/IonALPHA-L-GULURONATE
4MAW1Ligand/Ion4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:95 , GLN A:97 , GLU A:105 , ARG A:150 , HOH A:656 , HOH A:716 , HOH A:779 , HOH A:840BINDING SITE FOR RESIDUE LGU A 401
2AC2SOFTWAREGLN A:97 , THR A:139 , ALA A:140 , ASN A:141 , SER A:142 , ARG A:146 , ASN A:191 , ASN A:199 , TYR A:278 , LYS A:280 , HOH A:840BINDING SITE FOR RESIDUE BEM A 402
3AC3SOFTWAREASN A:141 , ARG A:146 , GLN A:189 , ASN A:191 , ASN A:199 , ALA A:200 , PRO A:202 , PHE A:284 , HOH A:790BINDING SITE FOR RESIDUE LGU A 403
4AC4SOFTWARESER A:142 , TYR A:144 , PRO A:202 , LYS A:205 , LYS A:218 , PHE A:284 , GLN A:286 , HOH A:736 , HOH A:822 , HOH A:842BINDING SITE FOR RESIDUE MAW A 404
5AC5SOFTWAREGLN A:97 , THR A:139 , ALA A:140 , ASN A:141 , ARG A:146 , ASN A:199 , TYR A:278 , LYS A:280 , HOH A:840BINDING SITE FOR RESIDUE LGU A 502
6AC6SOFTWAREPHE A:89 , ASP A:90 , GLN A:212 , TYR A:231 , THR A:233 , SER A:301 , LEU A:302 , HOH A:703 , HOH A:712 , HOH A:751BINDING SITE FOR RESIDUE GOL A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZAA)

(-) 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:232
 aligned with Q75WP3_9SPHN | Q75WP3 from UniProtKB/TrEMBL  Length:308

    Alignment length:232
                                                                                                                                                                                                                                                             308    
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       | -  
         Q75WP3_9SPHN    81 PAAAPGKNFDLSHWKLQLPDANTTEISSANLGLGYTSQYFYTDTDGAMTFWAPTTGGTTANSSYPRSELREMLDPSNSKVNWGWQGTHTMKLSGKTVQLPSSGKIIVAQIHGIMDDGTNAPPLVKAVFQDGQLDMQVKQNSDGTGSDVHNYFTGIKLGDLYNMEIRVTDGVAYVTMNGDTRSVDFVGKDAGWKNLKYYFKAGNYVQDNTSTGGSAIAKLYSLSVSHSN----   -
               SCOP domains d2zaaa_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Alginate_lyase2-2zaaA01 A:89-306                                                                                                                                                                                          ------ Pfam domains
         Sec.struct. author ...hhhhh.....eeee.......eehhhhhhh......eee.....eeeeee............eeeeee...............eeeeeeeeeeee......eeeeeeeee.....eeeeeeeeeee.eeeeeeee........ee..eeeee.....eeeeeeee..eeeeee..eeeeehhhhhhhhhhhheeeeeeeeee........eeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zaa A  81 PAAAPGKNFDLSHWKLQLPDANTTEISSANLGLGYTSQYFYTDTDGAMTFWAPTTGGTTANSSYPRSELREMLDPSNSKVNWGWQGTHTMKLSGKTVQLPSSGKIIVAQINGIMDDGTNAPPLVKAVFQDGQLDMQVKQNSDGTGSDVHNYFTGIKLGDLYNMEIRVTDGVAYVTMNGDTRSVDFVGKDAGWKNLKYYFKAGNFVQDNTSTGGSAIAKLYSLSVSHSNLEHH 312
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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 2ZAA)

(-) 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 2zab 2zac

(-) Related Entries Specified in the PDB File

2cws THE LIGAND FREE WILD-TYPE PROTEIN
2z42 THE LIGAND FREE WILD-TYPE PROTEIN
2za9
2zab
2zac