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(-) Description

Title :  STRUCTURE OF A GH3 B-GLUCOSIDASE FROM COW RUMEN METAGENOME IN COMPLEX WITH GALACTOSE
 
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 :  2.29
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase, Metagenome, B-Glicosidase, Functional Food, Prebiotics, Microbiota, Galactose, 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: ROSETTA2
    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, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GAL1Ligand/IonBETA-D-GALACTOSE
3SO48Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:59 , GLU A:143 , ASP A:532 , ARG A:538 , LEU A:583 , ARG A:597 , LYS A:630 , HIS A:631 , ARG A:641 , TYR A:677 , ASP A:709binding site for residue GAL A 1000
02AC2SOFTWAREARG A:450 , ARG A:694binding site for residue SO4 A 1001
03AC3SOFTWAREGLU A:281 , PHE A:282 , LYS A:388 , HOH A:1143binding site for residue SO4 A 1002
04AC4SOFTWARETYR A:394 , LYS A:395binding site for residue SO4 A 1003
05AC5SOFTWAREASN A:751 , SER A:754 , GLN A:755binding site for residue SO4 A 1004
06AC6SOFTWAREASN A:746binding site for residue SO4 A 1005
07AC7SOFTWAREVAL A:150 , ALA A:151 , LYS A:155binding site for residue SO4 A 1006
08AC8SOFTWARELYS A:54binding site for residue SO4 A 1007
09AC9SOFTWARESER A:517 , GLU A:518 , ARG A:521 , ALA A:744binding site for residue SO4 A 1008
10AD1SOFTWAREPRO A:114 , GLU A:115 , SER A:157 , THR A:159binding site for residue EDO A 1009
11AD2SOFTWAREPHE A:264 , GLU A:265 , LYS A:266 , SER A:267binding site for residue EDO A 1010

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K6O)

(-) 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 5K6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K6O)

(-) Exons   (0, 0)

(no "Exon" information available for 5K6O)

(-) 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:795
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhheeeee..........eeeeehhhhhh......hhhhh.......hhhhhhhhh...eehhhhhhhhhhhhhhh....................hhhhhhhhhhh..eeeeeee..................hhhhhhhhhhhhhhh..eeeeee......hhhhhhhh..eeee...hhhhhhhhhhhhhh............ee.hhhhh.hhhhh....eee.......hhhhhhhhh...eee..........eeeeeeeeeee....eeeeeeeeee........eeeeeee...........eeeeeee........eeeeeeeee.hhhheee.........eeee..eeeeeeee.....eeeeeeeee...eeeee...........eeeeeee.....eeeeeee......hhhhhhhhh.............hhhhhhhh..hhhhhhh..hhhhhhhhheee............eeee..hhhhhhh...eeeee..................hhhhhhhh.hhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhh...ee.eeee............eee.hhhhhhhh.hhhhhhhhhh....eeee...ee...hhhhhhhhhh...........eee.................hhhhhhhh....eeee..........hhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k6o A   4 EKVILDWNEYIEAARSVVSEGCVLLENNGTLPLEKGAVVSIFGRIQTHYYKSGTGSGGMVNVTHVVGVPEGLKLSEHVTVNEELENIYKEWEEENPFDEGLGWGTEPWSQPEMELTDEIVSNASAKSDVAIVIIGRTAGEDKDFSDVAGAYKLSETEEDMLRRVRKHFDKMVVLLNVGSLMDLNVISEINPDALMVIWQGGMIGGLGTADVLTGKVNPSGKLTDTIAYEINDYPSTENFGDPVRDYYAEDIYVGYRYFETFEKSKVRYPFGYGISYTEFEHTVGEFTADINSRTFTASCTVKNTGSVAGKDVAQFYVSAPQGKLGKPEKVLVAFKKTGILNPGKEEKITVTVPFDRFASFDDTGVTGAESCFVLEAGEYTVYEGKNVRESYKEGSFTLEENIVTEKLSKALAPMESFKRMKASENSDGTLSVKYEDVPVSDVDEKKRRLDNMPVEIPQDFTARYSLKDVLSGSVDMEKFIARLSDDDLACIVRGEGMGSSLVTAGTAAAFGGVSEYLRKMDIPAVCCDDGPSGMRLDSGATAFSMPNGTMLASTFNPDVIERMYGFTSLEMIYNKVECLLGPGMNIHRNPLNGRNFEYFSEDPYLNGTIASAMLKGLHKYGSDGVAKHFCCNNQELGRQACDSVVSQRALREIYLKGFEIAVKEGGCKAFMTTYAQVNGMWTAGNYDLNTRILRDEWGFKGIVMTDWWAQVNDRGGEPTKNNTAAMVRAQNDLYMVTANAAMNSANDNTLSQLSEGKLNRAELQRCAMNICEYAMNTMAMKRLCRNDIKVEIAGR 798
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793
   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 5K6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K6O)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5K6O)

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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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  5k6o
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  3.2.1.21
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 Related Entries

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

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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
5k6n CONTAINS THE SAME PROTEIN COMPLEXED WITH XYLOSE