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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT (D270A) BETA-GLUCOSIDASE FROM LISTERIA INNOCUA IN COMPLEX WITH CELLOBIOSE
 
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 :  2.00
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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1BGC4Ligand/IonBETA-D-GLUCOSE
2CBI1Ligand/IonCELLOBIOSE
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:238 , TRP A:271 , GLU A:473 , BGC A:802 , BGC A:803 , ARG B:572 , TYR B:583binding site for residue BGC A 801
2AC2SOFTWAREASP A:91 , PHE A:135 , ARG A:149 , LYS A:191 , HIS A:192 , MET A:235 , PHE A:238 , TRP A:271 , BGC A:801binding site for residue BGC A 802
3AC3SOFTWAREGLY A:408 , TRP A:409 , GLY A:472 , GLU A:473 , BGC A:801 , HOH A:972 , HOH A:982 , HOH A:1124 , TYR B:583binding site for residue BGC A 803
4AC4SOFTWAREARG A:143 , GLU A:214 , ASN A:218 , TYR A:564 , ASN A:566 , LEU A:568 , HOH A:901 , HOH A:903 , THR B:207 , HOH B:1036binding site for residue GOL A 804
5AC5SOFTWAREASP A:648 , THR A:650 , HOH A:968 , HOH A:1076 , HOH A:1134 , HOH A:1196binding site for residue MG A 805
6AC6SOFTWAREARG A:572 , TYR A:583 , PHE B:238 , TRP B:271 , GLU B:473 , CBI B:801binding site for residue BGC A 806
7AC7SOFTWARETYR A:583 , BGC A:806 , GLY B:408 , TRP B:409 , ASN B:410 , VAL B:411 , GLY B:472 , GLU B:473 , HOH B:915 , HOH B:943 , HOH B:971binding site for residue CBI B 801
8AC8SOFTWAREASP B:648 , THR B:650 , HOH B:934 , HOH B:949 , HOH B:970 , HOH B:1220binding site for residue MG B 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZO6)

(-) 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 4ZO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZO6)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZO6)

(-) 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:724
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.eeehhhhh.....hhhhhhhhhhhh..hhhhhh...eee...hhhhhhhhhhhhhhhh......eeee...........hhhhhhhh.hhhhhhhhhhhhhhhhhhh...ee............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhh............ee...hhhhhh.......hhhhhhhhhhhh....ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..............hhhhh.hhhhhhhhhhhhhhhheeeee.hhh.......eeeeee................hhhhh.hhhhhhhh...eeeeee......hhhhhhhhhhhhhhh.eeeeeee.hhhhh...........hhhhhhhhhhhhh....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
                 4zo6 A   1 MEQEKVQELVSQMTLDEKIAQCLQLSPFLFKGTNKNAELTGPLLQEMKLTDAHTENAGSVLGSSSALDMIGIQEAYLKTNRLGIPLVFMADVIHGYKTVFPIPLALGCSFDRETVRVMAEVSALEATADGHHVTFSPMLDLVRDPRWGRVMESTGEDPFLNSELGKAMVDGYQGDASKLNENLEQMAACVKHFAAYGAAEAGLEYNTVNMSTRELYQNYLPAYNAAIQAGAKLVMTAFNVVDGIPATMNKWLNRDVLRGEMEFDGVLISAWGAVAEVINHGTARNPKEAAQFSMEAGVDLEMMTTCYIHELKGLIEEGKLSENLLDEAVLRMLNLKNDLGLFEDPYRGLKNNDRTKDILTDESRGKARAAGVESAVLLENKSRLLPLAKEAKIALVGPLATSPDILGGWNVYGEEKDGINVETGLREVFETVEVVSTEYTELSEEDKVAVKAAVQNMDVVVLALGEKNEWGGEAGSLATIRLPEAQYQLAKFVQTLGKPVVITLFNGRPLEVKELAESSDALLELWFPGTEAGRVTADLLSGASNPSGKLSMSFPQTTGQIPVYYNHLRTGRPQTPENKGERYVSHYLDIPNEPFYPFGYGKSYSEFELKTSSLPKELNLGESLHVEVTIKNISDIAGKEVIQVYLQDVTASISRPVKELKAFEKVALQAGEEKTVTFELTSEAFSFYNHQLEKVQEPGLHRVFVGTSSEDVDVFEVEVGGYVL 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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720    


Chain B from PDB  Type:PROTEIN  Length:724
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               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...hhhhhh............ee...hhhhhh.......hhhhhhhhhhhhh...ee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.............hhhhhh.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
                 4zo6 B   1 MEQEKVQELVSQMTLDEKIAQCLQLSPFLFKGTNKNAELTGPLLQEMKLTDAHTENAGSVLGSSSALDMIGIQEAYLKTNRLGIPLVFMADVIHGYKTVFPIPLALGCSFDRETVRVMAEVSALEATADGHHVTFSPMLDLVRDPRWGRVMESTGEDPFLNSELGKAMVDGYQGDASKLNENLEQMAACVKHFAAYGAAEAGLEYNTVNMSTRELYQNYLPAYNAAIQAGAKLVMTAFNVVDGIPATMNKWLNRDVLRGEMEFDGVLISAWGAVAEVINHGTARNPKEAAQFSMEAGVDLEMMTTCYIHELKGLIEEGKLSENLLDEAVLRMLNLKNDLGLFEDPYRGLKNNDRTKDILTDESRGKARAAGVESAVLLENKSRLLPLAKEAKIALVGPLATSPDILGGWNVYGEEKDGINVETGLREVFETVEVVSTEYTELSEEDKVAVKAAVQNMDVVVLALGEKNEWGGEAGSLATIRLPEAQYQLAKFVQTLGKPVVITLFNGRPLEVKELAESSDALLELWFPGTEAGRVTADLLSGASNPSGKLSMSFPQTTGQIPVYYNHLRTGRPQTPENKGERYVSHYLDIPNEPFYPFGYGKSYSEFELKTSSLPKELNLGESLHVEVTIKNISDIAGKEVIQVYLQDVTASISRPVKELKAFEKVALQAGEEKTVTFELTSEAFSFYNHQLEKVQEPGLHRVFVGTSSEDVDVFEVEVGGYVL 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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720
   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 4ZO6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZO6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZO6)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

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