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(-) Description

Title :  CRYSTAL STRUCTURE OF PORPHYRANASE A (PORA) IN COMPLEX WITH NEO-PORPHYROTETRAOSE
 
Authors :  J. H. Hehemann, G. Correc, T. Barbeyron, W. Helbert, G. Michel, M. Czjze
Date :  07 Aug 09  (Deposition) - 07 Apr 10  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase Family Gh16, Beta-Sandwich Fold, Jelly Roll, Hydrolase-Carbohydrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Hehemann, G. Correc, T. Barbeyron, W. Helbert, M. Czjzek, G. Michel
Transfer Of Carbohydrate-Active Enzymes From Marine Bacteri To Japanese Gut Microbiota.
Nature V. 464 908 2010
PubMed-ID: 20376150  |  Reference-DOI: 10.1038/NATURE08937

(-) Compounds

Molecule 1 - PORPHYRANASE A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PFO4
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ZG2600
    Mutation: YES
    Organism Scientific: ZOBELLIA GALACTANIVORANS
    Organism Taxid: 63186
    Synonym: PORA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric/Biological Unit (7, 12)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4GAL1Ligand/IonBETA-D-GALACTOSE
5GLA1Ligand/IonALPHA D-GALACTOSE
6L6S2Ligand/Ion6-O-SULFO-ALPHA-L-GALACTOSE
7MG1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREL6S A:2 , ARG A:59 , TRP A:131 , SER A:139 , ASP A:141 , GLU A:144 , HIS A:167 , GLU A:234 , ALA A:241 , HOH A:287 , HOH A:466BINDING SITE FOR RESIDUE GLA A 1
02AC2SOFTWAREGLA A:1 , GAL A:3 , LYS A:27 , HIS A:53 , TRP A:56 , ARG A:59 , TRP A:131 , ARG A:133 , VAL A:134 , ILE A:230 , ASP A:274 , HOH A:333 , HOH A:455 , HOH A:545 , HOH A:600BINDING SITE FOR RESIDUE L6S A 2
03AC3SOFTWAREL6S A:2 , L6S A:4 , ASN A:25 , LYS A:27 , TRP A:56 , ARG A:133 , HOH A:333 , HOH A:516 , HOH A:600BINDING SITE FOR RESIDUE GAL A 3
04AC4SOFTWAREGAL A:3 , ASN A:25 , ASP A:40 , GLY A:41 , ASN A:42 , HOH A:421 , HOH A:547 , HOH A:578BINDING SITE FOR RESIDUE L6S A 4
05AC5SOFTWAREGLU A:38 , ASP A:40 , GLY A:74 , ASP A:265 , HOH A:356 , HOH A:372BINDING SITE FOR RESIDUE CA A 278
06AC6SOFTWAREASP A:51 , ALA A:69 , PHE A:70 , CL A:280 , HOH A:556BINDING SITE FOR RESIDUE MG A 279
07AC7SOFTWARESER A:43 , ILE A:44 , PHE A:70 , VAL A:71 , MG A:279 , HOH A:367BINDING SITE FOR RESIDUE CL A 280
08AC8SOFTWARELEU A:124 , SER A:125 , PRO A:249 , LYS A:250 , ASN A:253BINDING SITE FOR RESIDUE CL A 281
09AC9SOFTWAREASP A:148 , LYS A:250 , ASN A:253 , LYS A:259 , HOH A:582BINDING SITE FOR RESIDUE ACT A 282
10BC1SOFTWAREHIS A:167 , PRO A:177 , ALA A:241 , HOH A:302 , HOH A:461BINDING SITE FOR RESIDUE ACT A 283
11BC2SOFTWAREARG A:220 , HOH A:293BINDING SITE FOR RESIDUE ACT A 284
12BC3SOFTWARETRP A:266 , ARG A:268 , HOH A:521BINDING SITE FOR RESIDUE ACT A 285

(-) SS Bonds  (0, 0)

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

(-) 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 3ILF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ILF)

(-) 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:257
 aligned with PORA_ZOBGA | D7GXG0 from UniProtKB/Swiss-Prot  Length:510

    Alignment length:257
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       
           PORA_ZOBGA    18 AQLPSPTNGKKWEKVEQLSDEFNGNSIDTNKWYDYHPFWEGRAPSNFKKGNAFVSDGFLNLRSTLRKEPSSVQDPFKDIWVDAAAAVSKTKAQPGYYYEARFKASSLSMTSSFWFRVGQFSEIDVIEHIGNPSKENRQDDLPYQYHVNTHYYGKHAGLQPLGTEYKMPGRGRDNFYTYGFWWKSPNELLFYFNGKQVMRIVPRVPLDEELRMIFDTEVFPFATAGVANIGLPKPENLRDNSKNTMKVDWVRVYKLVD 274
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhheeee.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
                 3ilf A  18 AQLPSPTNGKKWEKVEQLSDEFDGNSIDTNKWYDYHPFWEGRAPSNFKKGDAFVSDGFLNLRSTLRKEPSSVQDPFKDIWVDAAAAVSKTKAQPGYYYEARFMASSLSMTSSFWFRVGQFSSIDVIEHIGDPSKENRQDDLPYQYHVNTHYYGKHAGLQPLGTEYKMPGRGRDNFYTYGFWWKSPNELLFYFNGKQVMRIVPRVPLDEELRMIFDTEVFPFATAGVANIGLPKPENLRDNSKNTMKVDWVRVYKLVD 274
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267
   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 3ILF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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        PORA_ZOBGA | D7GXG0: 4ate

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