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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDO-1,4-BETA-GLUCANASE FROM EISENIA FETIDA
 
Authors :  T. Arimori, T. Tamada
Date :  24 May 13  (Deposition) - 30 Oct 13  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  (Alpha/Alpha)6 Barrel Fold, Hydrolase, Sugar Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Arimori, A. Ito, M. Nakazawa, M. Ueda, T. Tamada
Crystal Structure Of Endo-1, 4-Beta-Glucanase From Eisenia Fetida
J. Synchrotron Radiat. V. 20 884 2013
PubMed-ID: 24121333  |  Reference-DOI: 10.1107/S0909049513021110

(-) Compounds

Molecule 1 - ENDO-1, 4-BETA-GLUCANASE
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZALPHAA
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 22-456
    Gene: EF-EG2
    Organism Common: BRANDLING WORM
    Organism Scientific: EISENIA FETIDA
    Organism Taxid: 6396

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FLC1Ligand/IonCITRATE ANION
3GOL5Ligand/IonGLYCEROL
4NA1Ligand/IonSODIUM ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:230 , ASP A:233 , GLU A:234 , ASN A:271 , HOH A:709 , HOH A:801BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREASP A:43 , LEU A:44 , ASP A:55 , HOH A:924 , HOH A:1087 , HOH A:1268BINDING SITE FOR RESIDUE NA A 502
3AC3SOFTWAREPHE A:225 , TYR A:226 , GLU A:431 , GOL A:505 , GOL A:509 , HOH A:741 , HOH A:831 , HOH A:843 , HOH A:1249BINDING SITE FOR RESIDUE TRS A 503
4AC4SOFTWAREGLU A:104 , GLY A:107 , GLN A:108 , TYR A:109 , ASN A:110 , HOH A:720 , HOH A:1229 , HOH A:1315BINDING SITE FOR RESIDUE FLC A 504
5AC5SOFTWAREASN A:141 , HIS A:144 , HIS A:378 , TYR A:427 , GLU A:431 , TRS A:503 , HOH A:975 , HOH A:1001BINDING SITE FOR RESIDUE GOL A 505
6AC6SOFTWAREASN A:195 , THR A:282 , THR A:288 , TYR A:339 , ILE A:341 , HOH A:790 , HOH A:893 , HOH A:996 , HOH A:1106BINDING SITE FOR RESIDUE GOL A 506
7AC7SOFTWARESER A:220 , TRP A:316 , GLN A:319 , PRO A:414 , ASP A:415 , ILE A:428 , ARG A:429 , HOH A:948 , HOH A:966 , HOH A:1260BINDING SITE FOR RESIDUE GOL A 507
8AC8SOFTWAREASP A:269 , TRP A:270 , ASN A:271 , TYR A:325 , HOH A:1075 , HOH A:1134BINDING SITE FOR RESIDUE GOL A 508
9AC9SOFTWARETRP A:270 , TRP A:320 , ARG A:324 , TRS A:503 , HOH A:843 , HOH A:1177 , HOH A:1239 , HOH A:1318BINDING SITE FOR RESIDUE GOL A 509

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:384 -A:391

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:387 -Pro A:388

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WC3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WC3)

(-) Exons   (0, 0)

(no "Exon" information available for 3WC3)

(-) 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:435
 aligned with I2FI81_EISFE | I2FI81 from UniProtKB/TrEMBL  Length:456

    Alignment length:435
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     
         I2FI81_EISFE    21 GQYNYDEVLEKSILFYEAERSGDLPANNRIPYRGDSALGDQGNQGQDLTGGWYDAGDHVKFGFPMAFATTTLAWGILEFRDGYEAAGQYNLALDSIRWTLNYFLKAHVSDNEFYGQVGDANTDHAYWGRPEDMTMERPAWSISPSAPGSDLAAETAAALAAGYLVFRDSDAAFANNLLAHSRTLYDFALNNRGIYSQSISNAAGFYASSAYEDELAWGAAWLYRATEEQEYLDRAYEFGTTTNTAWAYDWNEKIVGYQLLLTTSAGQTDFLPRVENFLRNWFPGGSVQYTPLGLAWLAQWGPNRYAANAAFIALVSAKYNILASESEQFARSQIHYMLGDAGRSYVVGFGNNPPQQPHHRSSSCPDQPAECDWDEFNQPGPNYQILYGALVGGPDQNDQFEDLRSDYIRNEVANDYNAGFQGAVAALRAIQLRDG 455
               SCOP domains d3wc3a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh........................................eehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhh..hhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....ee.....ee....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...................hhhhhh.......hhhhhhh..................................hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wc3 A  21 FQYNYDEVLEKSILFYEAERSGDLPANNRIPYRGDSALGDQGNQGQDLTGGWYDAGDHVKFGFPMAFATTTLAWGILEFRDGYEAAGQYNLALDSIRWTLNYFLKAHVSDNEFYGQVGDANTDHAYWGRPEDMTMERPAWSISPSAPGSDLAAETAAALAAGYLVFRDSDAAFANNLLAHSRTLYDFALNNRGIYSQSISNAAGFYASSAYEDELAWGAAWLYRATEEQEYLDRAYEFGTTTNTAWAYDWNEKIVGYQLLLTTSAGQTDFLPRVENFLRNWFPGGSVQYTPLGLAWLAQWGPNRYAANAAFIALVSAKYNILASESEQFARSQIHYMLGDAGRSYVVGFGNNPPQQPHHRSSSCPDQPAECDWDEFNQPGPNYQILYGALVGGPDQNDQFEDLRSDYIRNEVANDYNAGFQGAVAALRAIQLRDG 455
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450
   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 alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WC3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WC3)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (I2FI81_EISFE | I2FI81)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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