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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-GLUCOSIDASE FROM LISTERIA INNOCUA IN COMPLEX WITH GLUCONOLACTONE
 
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 :  2.40
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  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2LGC5Ligand/Ion(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
3MG2Ligand/IonMAGNESIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:91 , ARG A:149 , LYS A:191 , HIS A:192 , MET A:235 , PHE A:238 , ASP A:270 , TRP A:409 , GLU A:473 , GOL A:804binding site for residue LGC A 801
02AC2SOFTWARETHR A:212 , ASP A:242 , ASN A:249 , HOH A:922 , HIS B:690binding site for residue LGC A 802
03AC3SOFTWAREASP A:648 , THR A:650 , HOH A:928 , HOH A:955 , HOH A:1017binding site for residue MG A 803
04AC4SOFTWARETRP A:271 , GLU A:473 , LGC A:801 , HOH A:906 , ARG B:572 , TYR B:583binding site for residue GOL A 804
05AC5SOFTWAREGLU A:438 , TYR A:439 , THR A:440 , LYS A:467binding site for residue GOL A 805
06AC6SOFTWAREARG A:572 , TRP B:271 , GLU B:473 , LGC B:802 , HOH B:905binding site for residue GOL A 806
07AC7SOFTWARETHR A:207 , GLY A:243 , ARG B:143 , ARG B:213 , GLU B:214 , ASN B:218 , ASN B:566 , HOH B:907 , HOH B:979binding site for residue PEG B 801
08AC8SOFTWAREGOL A:806 , LEU B:61 , ASP B:91 , PHE B:135 , ARG B:149 , LYS B:191 , HIS B:192 , MET B:235 , PHE B:238 , ASP B:270 , GLU B:473binding site for residue LGC B 802
09AC9SOFTWAREHIS A:690 , THR B:212 , ASP B:242 , ASN B:249 , TRP B:251 , SO4 B:808 , HOH B:980 , HOH B:983binding site for residue LGC B 803
10AD1SOFTWARETYR A:583 , GLY B:408 , TRP B:409 , ASN B:410 , ASN B:468 , GLY B:472 , GLU B:473 , HOH B:905binding site for residue LGC B 804
11AD2SOFTWAREASP B:648 , THR B:650 , HOH B:942 , HOH B:966 , HOH B:969 , HOH B:994binding site for residue MG B 805
12AD3SOFTWARETRP B:470 , LEU B:477 , ARG B:481binding site for residue GOL B 806
13AD4SOFTWAREPRO B:158 , GLN B:217 , ASN B:218 , GLU B:659 , LYS B:661 , HOH B:931binding site for residue GOL B 807
14AD5SOFTWARESER A:211 , THR A:212 , HOH A:909 , SER B:211 , THR B:212 , LGC B:803 , HOH B:903binding site for residue SO4 B 808

(-) SS Bonds  (0, 0)

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

(-) 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 4ZOB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZOB)

(-) 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:722
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eeehhhhh........hhhhhhhhhh.hhhhhh...eee...hhhhhhhhhhhhhhh.......eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhh.......hhhhhhhh.hhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee...hhhhhh.......hhhhhhhhhhhh....ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..........hhhhhh.hhhhhhhhhhhhhhhheeeee.hhh........eeeee................hhhhh.hhhhhhhh....eeeee......hhhhhhhhhhhhhhh.eeeeeee.hhhhh...........hhhhhhhhhhhhh....eeeeee......hhhhhhh..eeee......hhhhhhhhhhhh..............hhhhh.............................................eeeee.....eeee...eeeeeeeee.....eeeeeeeeeee..........eeeeeeeeee....eeeeeeee......ee.....ee...eeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zob A   1 MEQEKVQELVSQMTLDEKIAQCLQLSPFLFKGTNKNAELTGPLLQEMKLTDAHTENAGSVLGSSSALDMIGIQEAYLKTNRLGIPLVFMADVIHGYKTVFPIPLALGCSFDRETVRVMAEVSALEATADGHHVTFSPMLDLVRDPRWGRVMESTGEDPFLNSELGKAMVDGYQGDASKLNENLEQMAACVKHFAAYGAAEAGLEYNTVNMSTRELYQNYLPAYNAAIQAGAKLVMTAFNVVDGIPATMNKWLNRDVLRGEMEFDGVLISDWGAVAEVINHGTARNPKEAAQFSMEAGVDLEMMTTCYIHELKGLIEEGKLSENLLDEAVLRMLNLKNDLGLFEDPYRGLNDRTKDILTDESRGKARAAGVESAVLLENKSRLLPLAKEAKIALVGPLATSPDILGGWNVYGEEKDGINVETGLREVFETVEVVSTEYTELSEEDKVAVKAAVQNMDVVVLALGEKNEWGGEAGSLATIRLPEAQYQLAKFVQTLGKPVVITLFNGRPLEVKELAESSDALLELWFPGTEAGRVTADLLSGASNPSGKLSMSFPQTTGQIPVYYNHLRTGRPQTPENKGERYVSHYLDIPNEPFYPFGYGKSYSEFELKTSSLPKELNLGESLHVEVTIKNISDIAGKEVIQVYLQDVTASISRPVKELKAFEKVALQAGEEKTVTFELTSEAFSFYNHQLEKVQEPGLHRVFVGTSSEDVDVFEVEVGGYVL 724
                                    10        20        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       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722  
                                                                                                                                                                                                                                                                                                                                                                                      349|                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                       352                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:721
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhheeehhhhh.....hhhhhhhhhhhh..hhhhhhh..eee...hhhhhhhhhhhhhhhh......eeee...........hhhhhhhh.hhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhh............eeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee...hhhhhh.......hhhhhhhhhhhhh...ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhhhhhhhhhhheeeee.hhh........eeeee................hhhhh.hhhhhhhh....eeeee......hhhhhhhhhhhhhhh.eeeeeee.hhhhh...........hhhhhhhhhhhhh....eeeeee......hhhhhhh..eeee......hhhhhhhhhhhh..............hhhhh.............................................eeeee.....eeee...eeeeeeeee.....eeeeeeeeeee..........eeeeeeeeee....eeeeeeeehhhhhhee.....ee...eeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zob B   1 MEQEKVQELVSQMTLDEKIAQCLQLSPFLFKGTNKNAELTGPLLQEMKLTDAHTENAGSVLGSSSALDMIGIQEAYLKTNRLGIPLVFMADVIHGYKTVFPIPLALGCSFDRETVRVMAEVSALEATADGHHVTFSPMLDLVRDPRWGRVMESTGEDPFLNSELGKAMVDGYQGDASKLNENLEQMAACVKHFAAYGAAEAGLEYNTVNMSTRELYQNYLPAYNAAIQAGAKLVMTAFNVVDGIPATMNKWLNRDVLRGEMEFDGVLISDWGAVAEVINHGTARNPKEAAQFSMEAGVDLEMMTTCYIHELKGLIEEGKLSENLLDEAVLRMLNLKNDLGLFEDPYRGLDRTKDILTDESRGKARAAGVESAVLLENKSRLLPLAKEAKIALVGPLATSPDILGGWNVYGEEKDGINVETGLREVFETVEVVSTEYTELSEEDKVAVKAAVQNMDVVVLALGEKNEWGGEAGSLATIRLPEAQYQLAKFVQTLGKPVVITLFNGRPLEVKELAESSDALLELWFPGTEAGRVTADLLSGASNPSGKLSMSFPQTTGQIPVYYNHLRTGRPQTPENKGERYVSHYLDIPNEPFYPFGYGKSYSEFELKTSSLPKELNLGESLHVEVTIKNISDIAGKEVIQVYLQDVTASISRPVKELKAFEKVALQAGEEKTVTFELTSEAFSFYNHQLEKVQEPGLHRVFVGTSSEDVDVFEVEVGGYVL 724
                                    10        20        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       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 
                                                                                                                                                                                                                                                                                                                                                                                      349|                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                       353
   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 4ZOB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  4zob
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  Q92AS9_LISIN | Q92AS9
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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