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(-) Description

Title :  STRUCTURE OF A GH3 B-GLUCOSIDASE FROM COW RUMEN METAGENOME
 
Authors :  M. Ramirez-Escudero, J. Sanz-Aparicio
Date :  25 May 16  (Deposition) - 05 Oct 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase, Metagenome, B-Glicosidase, Functional Food, Prebiotics, Microbiota, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Ramirez-Escudero, M. V. Del Pozo, J. Marin-Navarro, B. Gonzalez, P. N. Golyshin, J. Polaina, M. Ferrer, J. Sanz-Aparicio
Structural And Functional Characterization Of A Ruminal Beta-Glycosidase Defines A Novel Subfamily Of Glycoside Hydrolase Family 3 With Permuted Domain Topology.
J. Biol. Chem. V. 291 24200 2016
PubMed-ID: 27679487  |  Reference-DOI: 10.1074/JBC.M116.747527

(-) Compounds

Molecule 1 - B-GLUCOSIDASE
    Chains: A
    EC Number: 3.2.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA 2
    Expression System Vector: PLASMID
    Expression System Vector Type: PQE80L
    Gene: GLYA1
    Organism Scientific: METAGENOME
    Organism Taxid: 256318

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:59 , ASP A:532 , LEU A:583 , ARG A:597 , LYS A:630 , HIS A:631 , MET A:674 , ASP A:709 , TRP A:710 , GOL A:1005 , HOH A:1129 , HOH A:1147binding site for residue GOL A 1001
2AC2SOFTWAREVAL A:286 , GLY A:287 , GLU A:288 , GLU A:498 , SER A:503 , LEU A:504 , HOH A:1119 , HOH A:1123 , HOH A:1154 , HOH A:1335binding site for residue GOL A 1002
3AC3SOFTWAREASP A:358 , LYS A:659 , GLU A:662 , LYS A:666 , HOH A:1182 , HOH A:1493binding site for residue GOL A 1003
4AC4SOFTWAREARG A:168 , ASN A:193 , PRO A:194 , ASP A:195 , HOH A:1118 , HOH A:1145 , HOH A:1653binding site for residue GOL A 1004
5AC5SOFTWARESER A:59 , TRP A:106 , MET A:500 , ASP A:532 , ARG A:538 , GOL A:1001binding site for residue GOL A 1005
6AC6SOFTWARETRP A:711binding site for residue GOL A 1006
7AC7SOFTWAREALA A:251 , PHE A:420 , LYS A:421 , HOH A:1581binding site for residue GOL A 1007
8AC8SOFTWARETRP A:111 , PHE A:147 , SER A:148 , ALA A:153binding site for residue GOL A 1008
9AC9SOFTWAREGLU A:498 , GLY A:499 , MET A:500 , ALA A:741 , HOH A:1154binding site for residue GOL A 1009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K6L)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Leu A:34 -Pro A:35
2Gly A:499 -Met A:500
3Asp A:532 -Gly A:533
4Gly A:584 -Pro A:585
5Lys A:630 -His A:631
6Phe A:632 -Cys A:633
7Met A:738 -Val A:739

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K6L)

(-) Exons   (0, 0)

(no "Exon" information available for 5K6L)

(-) 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:794
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhheeeee.........eeeeeehhhhhh..................hhhhhhhhh..eeehhhhhhhhhhhhhhh....................hhhhhhhhhhh..eeeeeeee.................hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhh..eeee...hhhhhhhhhhhhhh............ee.hhhhh.hhhhh....eee.......hhhhhhhhh...eee..........eeeeeeeeeee....eeeeeeeeee........eeeeeee...........eeeeeee........eeeeeeeee.hhhheee.........eeee..eeeeeeee.....eeeeeeeee...eeeee...........eeeeeee.....eeeeeee......hhhhhhhhh.............hhhhhhh...hhhhhhh..hhhhhhhhheee............eeee..hhhhhhh...eeeee..................hhhhhhhh.hhhhhhhhhhhhhhhhhhh...ee..............hhhhh...hhhhhhhhhhhhhhhhhh...ee.................eee.hhhhhhhh.hhhhhhhhhh....eee....ee...hhhhhhhhhh...........eee.................hhhhhhhh....eeee..........hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k6l A   5 KVILDWNEYIEAARSVVSEGCVLLENNGTLPLEKGAVVSIFGRIQTHYYKSGTGSGGMVNVTHVVGVPEGLKLSEHVTVNEELENIYKEWEEENPFDEGLGWGTEPWSQPEMELTDEIVSNASAKSDVAIVIIGRTAGEDKDFSDVAGAYKLSETEEDMLRRVRKHFDKMVVLLNVGSLMDLNVISEINPDALMVIWQGGMIGGLGTADVLTGKVNPSGKLTDTIAYEINDYPSTENFGDPVRDYYAEDIYVGYRYFETFEKSKVRYPFGYGISYTEFEHTVGEFTADINSRTFTASCTVKNTGSVAGKDVAQFYVSAPQGKLGKPEKVLVAFKKTGILNPGKEEKITVTVPFDRFASFDDTGVTGAESCFVLEAGEYTVYEGKNVRESYKEGSFTLEENIVTEKLSKALAPMESFKRMKASENSDGTLSVKYEDVPVSDVDEKKRRLDNMPVEIPQDFTARYSLKDVLSGSVDMEKFIARLSDDDLACIVRGEGMGSSLVTAGTAAAFGGVSEYLRKMDIPAVCCDDGPSGMRLDSGATAFSMPNGTMLASTFNPDVIERMYGFTSLEMIYNKVECLLGPGMNIHRNPLNGRNFEYFSEDPYLNGTIASAMLKGLHKYGSDGVAKHFCCNNQELGRQACDSVVSQRALREIYLKGFEIAVKEGGCKAFMTTYAQVNGMWTAGNYDLNTRILRDEWGFKGIVMTDWWAQVNDRGGEPTKNNTAAMVRAQNDLYMVTANAAMNSANDNTLSQLSEGKLNRAELQRCAMNICEYAMNTMAMKRLCRNDIKVEIAGR 798
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794
   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 5K6L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K6L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K6L)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5K6L)

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  Cis Peptide Bonds
    Asp A:532 - Gly A:533   [ RasMol ]  
    Gly A:499 - Met A:500   [ RasMol ]  
    Gly A:584 - Pro A:585   [ RasMol ]  
    Leu A:34 - Pro A:35   [ RasMol ]  
    Lys A:630 - His A:631   [ RasMol ]  
    Met A:738 - Val A:739   [ RasMol ]  
    Phe A:632 - Cys A:633   [ RasMol ]  
 

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