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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-GLUCOSIDASE FROM LISTERIA INNOCUA IN COMPLEX WITH ISOFAGOMINE
 
Authors :  M. Nakajima, R. Yoshida, A. Miyanaga, K. Abe, Y. Takahashi, N. Sugimoto H. Toyoizumi, H. Nakai, M. Kitaoka, H. Taguchi
Date :  06 May 15  (Deposition) - 18 May 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Hydrolase, Beta-1, 2-Glucan Degradation, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nakajima, R. Yoshida, A. Miyanaga, K. Abe, Y. Takahashi, N. Sugimoto, H. Toyoizumi, H. Nakai, M. Kitaoka, H. Taguchi
Functional And Structural Analysis Of A Beta-Glucosidase Involved In Beta-1, 2-Glucan Metabolism In Listeria Innocua
Plos One V. 11 48870 2016
PubMed-ID: 26886583  |  Reference-DOI: 10.1371/JOURNAL.PONE.0148870

(-) Compounds

Molecule 1 - LIN1840 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LIN1840
    Mutation: YES
    Organism Scientific: LISTERIA INNOCUA SEROVAR 6A (STRAIN CLIP 11262)
    Organism Taxid: 272626
    Strain: CLIP 11262
    Synonym: BETA-GLUCOSIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1IFM2Ligand/Ion5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
2MG2Ligand/IonMAGNESIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:40 , ASP A:91 , PHE A:135 , ARG A:149 , LYS A:191 , HIS A:192 , ASP A:270 , GLU A:473 , HOH A:1000binding site for residue IFM A 801
2AC2SOFTWAREASP A:648 , THR A:650 , HOH A:930 , HOH A:997 , HOH A:1003 , HOH A:1144binding site for residue MG A 802
3AC3SOFTWARETRP A:470 , ARG A:481 , HOH A:1070 , LEU B:588 , HOH B:1178binding site for residue PEG B 801
4AC4SOFTWARETHR B:40 , ASP B:91 , PHE B:135 , ARG B:149 , LYS B:191 , HIS B:192 , ASP B:270 , GLU B:473 , HOH B:1081binding site for residue IFM B 802
5AC5SOFTWAREASP B:648 , THR B:650 , HOH B:933 , HOH B:961 , HOH B:985 , HOH B:1128binding site for residue MG B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZOA)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Ser A:136 -Pro A:137
2Lys A:191 -His A:192
3Phe A:193 -Ala A:194
4Leu A:385 -Pro A:386
5Ile A:561 -Pro A:562
6Ser B:136 -Pro B:137
7Lys B:191 -His B:192
8Phe B:193 -Ala B:194
9Leu B:385 -Pro B:386
10Ile B:561 -Pro B:562

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZOA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZOA)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZOA)

(-) 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:716
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eeehhhhh...........hhhhhh...eee...hhhhhhhhhhhhhhhh......eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee...hhhhhh.......hhhhhhhhhhhhh...ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..............hhhhh.hhhhhhhhhhhhhhhheeeee.hhh........eeeee................hhhhh.hhhhhhhh....eeeee......hhhhhhhhhhhhhhh.eeeeeee.hhhhh...........hhhhhhhhhhhhhh...eeeeee......hhhhhh...eeee......hhhhhhhhhhh...............hhhhh.............................................eeeee.....eeee...eeeeeeeee.....eeeeeeeeeee..........eeeeeeeeee....eeeeeeeehhhhhhee.....ee...eeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zoa A   1 MEQEKVQELVSQMTLDEKIAQCLQLSPFLFKLTGPLLEMKLTDAHTENAGSVLGSSSALDMIGIQEAYLKTNRLGIPLVFMADVIHGYKTVFPIPLALGCSFDRETVRVMAEVSALEATADGHHVTFSPMLDLVRDPRWGRVMESTGEDPFLNSELGKAMVDGYQGDASKLNENLEQMAACVKHFAAYGAAEAGLEYNTVNMSTRELYQNYLPAYNAAIQAGAKLVMTAFNVVDGIPATMNKWLNRDVLRGEMEFDGVLISDWGAVAEVINHGTARNPKEAAQFSMEAGVDLEMMTTCYIHELKGLIEEGKLSENLLDEAVLRMLNLKNDLGLFEDPYRGLKNNDRTKDILTDESRGKARAAGVESAVLLENKSRLLPLAKEAKIALVGPLATSPDILGGWNVYGEEKDGINVETGLREVFETVEVVSTEYTELSEEDKVAVKAAVQNMDVVVLALGEKNEWGGEAGSLATIRLPEAQYQLAKFVQTLGKPVVITLFNGRPLEVKELAESSDALLELWFPGTEAGRVTADLLSGASNPSGKLSMSFPQTTGQIPVYYNHLRTGRPQTPENKGERYVSHYLDIPNEPFYPFGYGKSYSEFELKTSSLPKELNLGESLHVEVTIKNISDIAGKEVIQVYLQDVTASISRPVKELKAFEKVALQAGEEKTVTFELTSEAFSFYNHQLEKVQEPGLHRVFVGTSSEDVDVFEVEVGGYVL 724
                                    10        20        30||    ||48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718      
                                                         31|   44|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                                          39    46                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:715
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhheeehhhhh..........hhhhhhhh.eee...hhhhhhhhhhhhhhhh......eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee...hhhhhhhhhh...hhhhhhhhhhhhh...ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..............hhhhh.hhhhhhhhhhhhhhhheeeee.hhh........eeeee................hhhhh.hhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh.eeeeeee.hhhhh...........hhhhhhhhhhhhhh...eeeeee......hhhhhhh..eeee......hhhhhhhhhhh...............hhhhh.............hhhhh...........................eeeee.....eeee...eeeeeeeee.....eeeeeeeeeee..........eeeeeeeeee....eeeeeeee......ee.....ee...eeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zoa B   1 MEQEKVQELVSQMTLDEKIAQCLQLSPFLFLTGPLLEMKLTDAHTENAGSVLGSSSALDMIGIQEAYLKTNRLGIPLVFMADVIHGYKTVFPIPLALGCSFDRETVRVMAEVSALEATADGHHVTFSPMLDLVRDPRWGRVMESTGEDPFLNSELGKAMVDGYQGDASKLNENLEQMAACVKHFAAYGAAEAGLEYNTVNMSTRELYQNYLPAYNAAIQAGAKLVMTAFNVVDGIPATMNKWLNRDVLRGEMEFDGVLISDWGAVAEVINHGTARNPKEAAQFSMEAGVDLEMMTTCYIHELKGLIEEGKLSENLLDEAVLRMLNLKNDLGLFEDPYRGLKNNDRTKDILTDESRGKARAAGVESAVLLENKSRLLPLAKEAKIALVGPLATSPDILGGWNVYGEEKDGINVETGLREVFETVEVVSTEYTELSEEDKVAVKAAVQNMDVVVLALGEKNEWGGEAGSLATIRLPEAQYQLAKFVQTLGKPVVITLFNGRPLEVKELAESSDALLELWFPGTEAGRVTADLLSGASNPSGKLSMSFPQTTGQIPVYYNHLRTGRPQTPENKGERYVSHYLDIPNEPFYPFGYGKSYSEFELKTSSLPKELNLGESLHVEVTIKNISDIAGKEVIQVYLQDVTASISRPVKELKAFEKVALQAGEEKTVTFELTSEAFSFYNHQLEKVQEPGLHRVFVGTSSEDVDVFEVEVGGYVL 724
                                    10        20        30|    || 49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719     
                                                        30|   44|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                                         39    46
   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 4ZOA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZOA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZOA)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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    Phe A:193 - Ala A:194   [ RasMol ]  
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 Related Entries

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UniProtKB/TrEMBL
        Q92AS9_LISIN | Q92AS9: 4zo6 4zo7 4zo8 4zo9 4zob 4zoc 4zod 4zoe

(-) Related Entries Specified in the PDB File

4zo6 4zo7 4zo8 4zo9 4zob 4zoc 4zod 4zoe