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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF BETA-AGARASE A FROM ZOBELLIA GALACTANIVORANS
 
Authors :  J. Allouch, M. Jam, W. Helbert, T. Barbeyron, B. Kloareg, B. Henrissat, M. Czjzek
Date :  29 Jul 03  (Deposition) - 09 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Agarase, Glycoside Hydrolase Family 16, Agarose Degradation, Cleavage Of Beta-1, 4-D-Galactose Linkages (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Allouch, M. Jam, W. Helbert, T. Barbeyron, B. Kloareg, B. Henrissat, M. Czjzek
The Three-Dimensional Structures Of Two {Beta}-Agarases.
J. Biol. Chem. V. 278 47171 2003
PubMed-ID: 12970344  |  Reference-DOI: 10.1074/JBC.M308313200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-AGARASE A
    Chains: A
    EC Number: 3.2.1.81
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ZOBELLIA GALACTANIVORANS
    Organism Taxid: 63186
    Strain: DSIJ

 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
1CA1Ligand/IonCALCIUM ION
2NA1Ligand/IonSODIUM ION
3SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:161BINDING SITE FOR RESIDUE NA A 600
2AC2SOFTWAREASP A:22 , SER A:47 , ASN A:49 , SER A:91 , ASP A:279 , HOH A:902BINDING SITE FOR RESIDUE CA A 700
3AC3SOFTWAREASN A:31 , LYS A:125 , TYR A:208 , GLU A:216 , TYR A:218 , LYS A:223 , HOH A:798 , HOH A:837 , HOH A:838 , HOH A:1017BINDING SITE FOR RESIDUE SO4 A 500
4AC4SOFTWARETYR A:50 , THR A:51 , GLY A:90 , ARG A:229 , HOH A:760 , HOH A:794 , HOH A:878 , HOH A:879 , HOH A:1050 , HOH A:1055BINDING SITE FOR RESIDUE SO4 A 501
5AC5SOFTWAREGLN A:117 , TYR A:118 , PRO A:178 , PHE A:179 , ASN A:244 , HOH A:910BINDING SITE FOR RESIDUE SO4 A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O4Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:118 -Pro A:119
2Asn A:177 -Pro A:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O4Y)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH16_2PS51762 Glycosyl hydrolases family 16 (GH16) domain profile.AGAA_ZOBGA21-289  1A:21-289

(-) Exons   (0, 0)

(no "Exon" information available for 1O4Y)

(-) 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:270
 aligned with AGAA_ZOBGA | G0L322 from UniProtKB/Swiss-Prot  Length:539

    Alignment length:270
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
           AGAA_ZOBGA    20 AQDWNGIPVPANPGNGMTWQLQDNVSDSFNYTSSEGNRPTAFTSKWKPSYINGWTGPGSTIFNAPQAWTNGSQLAIQAQPAGNGKSYNGIITSKNKIQYPVYMEIKAKIMDQVLANAFWTLTDDETQEIDIMEGYGSDRGGTWFAQRMHLSHHTFIRNPFTDYQPMGDATWYYNGGTPWRSAYHRYGCYWKDPFTLEYYIDGVKVRTVTRAEIDPNNHLGGTGLNQATNIIIDCENQTDWRPAATQEELADDSKNIFWVDWIRVYKPVAV 289
               SCOP domains d1o4ya_ A: beta-Agarase A                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1o4yA00 A:20-289  [code=2.60.120.200, no name defined]                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................eeeee.hhhh.....ee.....hhhhhh.ee............eee....eeee...eeeeeeeee..eeee.eeee.......eeeeeeee......eeeeeee.....eeeeeeeee.hhhhhhhhhheeeeeeeeee....eee...hhh.eee....hhhhh.eeeeeeeee..eeeeee..eeeeeehhhhhh..............eeeeeee.........hhhhhhh....eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -GH16_2  PDB: A:21-289 UniProt: 21-289                                                                                                                                                                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1o4y A  20 AQDWNGIPVPANPGNGMTWQLQDNVSDSFNYTSSEGNRPTAFTSKWKPSYINGWTGPGSTIFNAPQAWTNGSQLAIQAQPAGNGKSYNGIITSKNKIQYPVYMEIKAKIMDQVLANAFWTLTDDETQEIDIMEGYGSDRGGTWFAQRMHLSHHTFIRNPFTDYQPMGDATWYYNGGTPWRSAYHRYGCYWKDPFTLEYYIDGVKVRTVTRAEIDPNNHLGGTGLNQATNIIIDCENQTDWRPAATQEELADDSKNIFWVDWIRVYKPVAV 289
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O4Y)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AGAA_ZOBGA | G0L322)
molecular function
    GO:0033916    beta-agarase activity    Catalysis of the hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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        AGAA_ZOBGA | G0L322: 1urx

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