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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF BETA-PORPHYRANASE A FROM ZOBELLIA GALACTANIVORANS
 
Authors :  J. H. Hehemann, G. Correc, M. Jam, G. Michel, M. Czjzek
Date :  06 May 12  (Deposition) - 25 Jul 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Agar Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Hehemann, G. Correc, F. Thomas, T. Bernard, T. Barbeyron, M. Jam, W. Helbert, G. Michel, M. Czjzek
Biochemical And Structural Characterization Of The Complex Agarolytic Enzyme System From The Marine Bacterium Zobellia Galactanivorans.
J. Biol. Chem. V. 287 30571 2012
PubMed-ID: 22778272  |  Reference-DOI: 10.1074/JBC.M112.377184
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-PORPHYRANASE A
    Chains: A
    EC Number: 3.2.1.178
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PFO4
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, RESIDUES 18-277
    Organism Scientific: ZOBELLIA GALACTANIVORANS
    Organism Taxid: 63186
    Other Details: ISOLATED FROM THE RED ALGAE DELESSERIA SANGUINEA AND DEPOSITED AT THE GERMAN COLLECTION OF MICROORGANISMS (DSM)
    Synonym: BETA-PORPHYRANASE A, FAMILY GH16

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:38 , ASN A:40 , GLY A:74 , ASP A:265 , HOH A:2061 , HOH A:2068BINDING SITE FOR RESIDUE CA A1275
2AC2SOFTWAREHIS A:167 , PRO A:177 , GLY A:242 , LYS A:271 , HOH A:2016 , HOH A:2317 , HOH A:2318 , HOH A:2411 , HOH A:2449 , HOH A:2450BINDING SITE FOR RESIDUE SO4 A1276
3AC3SOFTWARELEU A:124 , SER A:125 , PRO A:249 , LYS A:250 , ASN A:253BINDING SITE FOR RESIDUE CL A1277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ATE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:60 -Pro A:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ATE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ATE)

(-) Exons   (0, 0)

(no "Exon" information available for 4ATE)

(-) 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:256
 aligned with PORA_ZOBGA | D7GXG0 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:256
                                    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      
           PORA_ZOBGA    20 LPSPTNGKKWEKVEQLSDEFNGNSIDTNKWYDYHPFWEGRAPSNFKKGNAFVSDGFLNLRSTLRKEPSSVQDPFKDIWVDAAAAVSKTKAQPGYYYEARFKASSLSMTSSFWFRVGQFSEIDVIEHIGNPSKENRQDDLPYQYHVNTHYYGKHAGLQPLGTEYKMPGRGRDNFYTYGFWWKSPNELLFYFNGKQVMRIVPRVPLDEELRMIFDTEVFPFATAGVANIGLPKPENLRDNSKNTMKVDWVRVYKLVDG 275
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.hhhh............ee...........eee....eeee..eeeee.ee..hhhhh........eee.eeee........eeeeeee......eeeeeee....eeeeeeeee....hhhhh.hhh.eeeeeeee.hhhh......eeee...hhhhh.eeeeeeeee..eeeeee..eeeeee..........eeeee.................hhhhhh.....eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ate A  20 LPSPTNGKKWEKVEQLSDEFNGNSIDTNKWYDYHPFWEGRAPSNFKKGNAFVSDGFLNLRSTLRKEPSSVQDPFKDIWVDAAAAVSKTKAQPGYYYEARFKASSLSMTSSFWFRVGQFSEIDVIEHIGNPSKENRQDDLPYQYHVNTHYYGKHAGLQPLGTEYKMPGRGRDNFYTYGFWWKSPNELLFYFNGKQVMRIVPRVPLDEELRMIFDTEVFPFATAGVANIGLPKPENLRDNSKNTMKVDWVRVYKLVDG 275
                                    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
   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 4ATE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ATE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ATE)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PORA_ZOBGA | D7GXG0)
molecular function
    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: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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    Ala A:60 - Pro A:61   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PORA_ZOBGA | D7GXG0: 3ilf

(-) Related Entries Specified in the PDB File

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