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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-GLUCOSIDASE FROM LISTERIA INNOCUA IN COMPLEX WITH GLUCOSE
 
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 :  2.10
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, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GOL7Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:91 , PHE A:135 , ARG A:149 , LYS A:191 , HIS A:192 , MET A:235 , PHE A:238 , ASP A:270 , GLU A:473 , GOL A:803binding site for residue BGC A 801
02AC2SOFTWAREASP A:648 , THR A:650 , HOH A:956 , HOH A:989 , HOH A:994 , HOH A:1072binding site for residue MG A 802
03AC3SOFTWARETRP A:271 , GLU A:473 , BGC A:801 , HOH A:976 , ARG B:572binding site for residue GOL A 803
04AC4SOFTWAREARG A:143 , GLU A:214 , ASN A:218 , TYR A:564 , ASN A:566 , LEU A:568 , HOH A:906 , HOH A:957 , HOH A:1008 , THR B:207binding site for residue GOL A 804
05AC5SOFTWAREGLU A:438 , TYR A:439 , THR A:440 , LYS A:467binding site for residue GOL A 805
06AC6SOFTWARETRP A:470 , ARG A:481 , LEU A:482 , PRO A:483 , HOH B:960binding site for residue PEG A 806
07AC7SOFTWARESER A:211 , THR A:212 , HOH A:932 , THR B:212 , HOH B:928binding site for residue SO4 A 807
08AC8SOFTWAREARG A:572 , TYR A:583 , HOH A:903 , HOH A:905 , TRP B:271 , GLU B:473 , BGC B:802binding site for residue GOL A 808
09AC9SOFTWARETHR A:212 , ASN A:249 , TRP A:251 , HIS B:690 , HOH B:911 , HOH B:970 , HOH B:1071binding site for residue PEG B 801
10AD1SOFTWAREGOL A:808 , 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 BGC B 802
11AD2SOFTWAREHIS A:690 , THR B:212 , ASP B:242 , ILE B:244 , ASN B:249 , TRP B:251 , HOH B:948 , HOH B:984binding site for residue BGC B 803
12AD3SOFTWAREASP B:648 , THR B:650 , HOH B:947 , HOH B:990 , HOH B:1028 , HOH B:1091binding site for residue MG B 804
13AD4SOFTWARETHR A:207 , ASN A:209 , ARG B:143 , GLU B:214 , ASN B:218 , TYR B:564 , ASN B:566 , LEU B:568 , HOH B:909 , HOH B:1072binding site for residue GOL B 805
14AD5SOFTWARELEU B:220 , GLU B:260 , MET B:261 , HOH B:983binding site for residue GOL B 806
15AD6SOFTWAREGLU B:438 , TYR B:439 , THR B:440 , LYS B:467binding site for residue GOL B 807

(-) SS Bonds  (0, 0)

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

(-) 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 4ZOD)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZOD)

(-) 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:720
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhh.eeehhhhh........hhhhhhhhh..hhhhhhh..eee...hhhhhhhhhhhhhhh.......eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhh.......hhhhhhhh.hhhhhhhhhh...eeee...ee..ee...hhhhhh...........eee...hhhhhh.......hhhhhhhhhhhh....ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........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
                 4zod A   1 MEQEKVQELVSQMTLDEKIAQCLQLSPFLFKGTNKNAELTGPLLQEMKLTDAHTENAGSVLGSSSALDMIGIQEAYLKTNRLGIPLVFMADVIHGYKTVFPIPLALGCSFDRETVRVMAEVSALEATADGHHVTFSPMLDLVRDPRWGRVMESTGEDPFLNSELGKAMVDGYQGDASKLNENLEQMAACVKHFAAYGAAEAGLEYNTVNMSTRELYQNYLPAYNAAIQAGAKLVMTAFNVVDGIPATMNKWLNRDVLRGEMEFDGVLISDWGAVAEVINHGTARNPKEAAQFSMEAGVDLEMMTTCYIHELKGLIEEGKLSENLLDEAVLRMLNLKNDLGLFEDPYRGLRTKDILTDESRGKARAAGVESAVLLENKSRLLPLAKEAKIALVGPLATSPDILGGWNVYGEEKDGINVETGLREVFETVEVVSTEYTELSEEDKVAVKAAVQNMDVVVLALGEKNEWGGEAGSLATIRLPEAQYQLAKFVQTLGKPVVITLFNGRPLEVKELAESSDALLELWFPGTEAGRVTADLLSGASNPSGKLSMSFPQTTGQIPVYYNHLRTGRPQTPENKGERYVSHYLDIPNEPFYPFGYGKSYSEFELKTSSLPKELNLGESLHVEVTIKNISDIAGKEVIQVYLQDVTASISRPVKELKAFEKVALQAGEEKTVTFELTSEAFSFYNHQLEKVQEPGLHRVFVGTSSEDVDVFEVEVGGYVL 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       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
                                                                                                                                                                                                                                                                                                                                                                                      349|                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                                                                                                                       354                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:721
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eeehhhhh.....hhhhhhhhhhhh..hhhhhh...eee...hhhhhhhhhhhhhhhh......eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhhh..........eee...hhhhhh.......hhhhhhhhhhhhh...ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhhhhhhhhhhheeeee.hhh........eeeee................hhhhh.hhhhhhhh....eeeee......hhhhhhhhhhhhhhh.eeeeeee.hhhhh...........hhhhhhhhhhhhh....eeeeee......hhhhhh...eeee......hhhhhhhhhhhh..............hhhhh.............................................eeeee.....eeee...eeeeeeeee.....eeeeeeeeeee..........eeeeeeeeee....eeeeeeeehhhhhhee.....ee...eeeeeeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zod 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)
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    → 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 4ZOD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4zob 4zoc 4zoe

(-) Related Entries Specified in the PDB File

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