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(-) Description

Title :  STRUCTURE OF A GH3 B-GLICOSIDASE FROM COW RUMEN METAGENOME IN COMPLEXED WITH XYLOSE
 
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 :  2.08
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase, Metagenome, B-Glicosidase, Functional Food, Prebiotics, Microbiota, Xylose, 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
    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  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
3XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:59 , GLU A:143 , ASP A:532 , LEU A:583 , ARG A:597 , LYS A:630 , HIS A:631 , ARG A:641 , MET A:674 , TYR A:677 , ASP A:709 , HOH A:1326binding site for residue XYP A 1000
02AC2SOFTWARESER A:517 , GLU A:518 , ARG A:521 , ALA A:744 , HOH A:1103binding site for residue SO4 A 1001
03AC3SOFTWAREASN A:746 , HOH A:1264binding site for residue SO4 A 1002
04AC4SOFTWAREPRO A:323 , GLN A:324 , HOH A:1126 , HOH A:1324binding site for residue SO4 A 1003
05AC5SOFTWARETYR A:385 , TYR A:394 , LYS A:395binding site for residue SO4 A 1004
06AC6SOFTWAREGLU A:281 , PHE A:282 , LYS A:388 , HOH A:1181 , HOH A:1185 , HOH A:1339binding site for residue SO4 A 1005
07AC7SOFTWAREARG A:450 , ARG A:694 , GOL A:1009 , HOH A:1317 , HOH A:1348binding site for residue SO4 A 1006
08AC8SOFTWAREASP A:358 , LYS A:659 , GLU A:662 , ILE A:663 , LYS A:666 , HOH A:1253 , HOH A:1347binding site for residue GOL A 1007
09AC9SOFTWAREPRO A:356 , ASP A:358 , ARG A:359 , HOH A:1253 , HOH A:1300binding site for residue GOL A 1008
10AD1SOFTWAREVAL A:445 , ASP A:446 , LYS A:449 , ARG A:450 , ASP A:453 , SO4 A:1006 , HOH A:1135 , HOH A:1320binding site for residue GOL A 1009
11AD2SOFTWAREPRO A:114 , GLU A:115 , SER A:157 , GLU A:158 , THR A:159binding site for residue GOL A 1010
12AD3SOFTWAREVAL A:150 , ALA A:151 , LYS A:155binding site for residue GOL A 1011

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K6N)

(-) 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 5K6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K6N)

(-) Exons   (0, 0)

(no "Exon" information available for 5K6N)

(-) 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:792
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhheeeee.........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............hhhhhhh...hhhhhhhhhhhhhhhhhh...ee.eeee............eee.hhhhhhhh.hhhhhhhhhh....eeee...ee...hhhhhhhhhh...........eee.................hhhhhhhh....eeee..........hhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k6n A   3 IEKVILDWNEYIEAARSVVSEGCVLLENNGTLPLEKGAVVSIFGRIQTHYYKSGTGSGGMVNVTHVVGVPEGLKLSEHVTVNEELENIYKEWEEENPFDEGTEPWSQPEMELTDEIVSNASAKSDVAIVIIGRTAGEDKDFSDVAGAYKLSETEEDMLRRVRKHFDKMVVLLNVGSLMDLNVISEINPDALMVIWQGGMIGGLGTADVLTGKVNPSGKLTDTIAYEINDYPSTENFGDPVRDYYAEDIYVGYRYFETFEKSKVRYPFGYGISYTEFEHTVGEFTADINSRTFTASCTVKNTGSVAGKDVAQFYVSAPQGKLGKPEKVLVAFKKTGILNPGKEEKITVTVPFDRFASFDDTGVTGAESCFVLEAGEYTVYEGKNVRESYKEGSFTLEENIVTEKLSKALAPMESFKRMKASENSDGTLSVKYEDVPVSDVDEKKRRLDNMPVEIPQDFTARYSLKDVLSGSVDMEKFIARLSDDDLACIVRGEGMGSSLVTAGTAAAFGGVSEYLRKMDIPAVCCDDGPSGMRLDSGATAFSMPNGTMLASTFNPDVIERMYGFTSLEMIYNKVECLLGPGMNIHRNPLNGRNFEYFSEDPYLNGTIASAMLKGLHKYGSDGVAKHFCCNNQELGRQACDSVVSQRALREIYLKGFEIAVKEGGCKAFMTTYAQVNGMWTAGNYDLNTRILRDEWGFKGIVMTDWWAQVNDRGGEPTKNNTAAMVRAQNDLYMVTANAAMNSANDNTLSQLSEGKLNRAELQRCAMNICEYAMNTMAMKRLCRNDIKVEIAGR 798
                                    12        22        32        42        52        62        72        82        92       102||     116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796  
                                                                                                                              103|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                               108
   Legend:   → Mismatch (orange background)
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  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 5K6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K6N)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5K6N)

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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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  5k6n
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 Related Entries

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(-) Related Entries Specified in the PDB File

5k6l CONTAINS THE SAME PROTEIN COMPLEXED WITH GLYCEROL
5k6m CONTAINS THE SAME PROTEIN COMPLEXED WITH GLUCOSE