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(-) Description

Title :  FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH PUGNAC
 
Authors :  E. Ficko-Blean, K. A. Stubbs, O. Berg, D. J. Vocadlo, A. B. Boraston
Date :  19 Sep 07  (Deposition) - 18 Mar 08  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Mucopolysaccharidosis, Alpha-N-Acetylglucosaminidase, Family 89 Glycoside Hydrolase, Hydrolase, Gh89, Naglu, Pugnac, Sanfilippo Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ficko-Blean, K. A. Stubbs, O. Nemirovsky, D. J. Vocadlo, A. B. Boraston
Structural And Mechanistic Insight Into The Basis Of Mucopolysaccharidosis Iiib.
Proc. Natl. Acad. Sci. Usa V. 105 6560 2008
PubMed-ID: 18443291  |  Reference-DOI: 10.1073/PNAS.0711491105

(-) Compounds

Molecule 1 - ALPHA-N-ACETYLGLUCOSAMINIDASE
    Atcc: 13124
    Chains: A
    EC Number: 3.2.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 26-916
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2OAN1Ligand/IonO-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE)AMINO-N-PHENYLCARBAMATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:299 , CYS A:301 , TYR A:305 , TRP A:366 , MET A:369 , HIS A:482 , GLU A:483 , TRP A:517 , LEU A:540 , PHE A:566 , GLU A:601 , GLN A:664 , LEU A:822 , TYR A:825 , HOH A:2137 , HOH A:2338BINDING SITE FOR RESIDUE OAN A1911
2AC2SOFTWARELEU A:48 , ASP A:51 , ASP A:53 , THR A:56 , ALA A:148 , GLU A:149BINDING SITE FOR RESIDUE CA A1912

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VCB)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:26 -Val A:27
2Gly A:377 -Pro A:378
3Asn A:520 -Pro A:521
4Asn A:748 -Gly A:749

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VCB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VCB)

(-) Exons   (0, 0)

(no "Exon" information available for 2VCB)

(-) 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:883
 aligned with A0A0H2YU91_C | A0A0H2YU91 from UniProtKB/TrEMBL  Length:2095

    Alignment length:885
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905     
         A0A0H2YU91_C    26 GVEITEGVTVTAKGNTEGNTADLAIDGDLSTYWESSNDYKWIEVDLGGIYELSKIEIFNKDEAVYKYNIYASEDGENFNKIAYKNNDNVSDSNGNMHTIDNVRAGKIRIDVVQNSNSDRVNIAEINVFGKNTGESLPEVKKIATSNFSETPWATEYEKFNSDSAYANEKTLNEIKNLVGRVIGREFKDKFIFEIRDQLNGNDVFEVSDSGDGKVLIKGNNGVSLASGFNYYLKNYCNVSYNPIMGSNLKMPETMPSVGERVVIDTPYEHRYALNFCTYSYTMSFWDWDQYEEFLDWCAMNGVNLVLDIIGQEEVLRRTLNEFGYSDEEVKEFISGPAYFAWFYMQNMTGFGGPLPNDWFEQRAELGRKMHDRMQSFGINPVLQGYSGMVPRDFKEKNQEAQTISQGGWCGFDRPDMLKTYVNEGEADYFQKVADVFYEKQKEVFGDVTNFYGVDPFHEGGNTGDLDNGKIYEIIQNKMIEHDNDAVWVIQNWQGNPSNNKLEGLTKKDQAMVLDLFSEVSPDWNRLEERDLPWIWNMLHNFGGRMGMDAAPEKLATEIPKALANSEHMVGIGITPEAINTNPLAYELLFDMAWTRDQINFRTWTEDYIERRYGKTNKEILEAWNIILDTAYKKRNDYYQGAAESIINARPGFGIKSASTWGHSKIVYDKSEFEKAIEIFAKNYDEFKDSDAFLYDFADILKQLLANSAQEYYEVMCNAYNNGNGEKFKFVSGKFLELIKLQERVLSTRPEFLIGNWIEDARTMLKDSDDWTKDLFEFNARALVTTWGSRNNADGGGLKDYSNRQWSGLTEDYYYARWEKWINGLQAELDGGAKAPNIDWFKMEYDWVNKKSDTDKLYPTEASNENLGELAKIAMESYSVTNMDKI 910
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.......hhhhhh.......ee......eeeeeeeeeeeeeeeeee......eeeeeeee......eeeeee..........eeeeeeeeeeeeeeeeeeee......ee.eeeeeeee.......-......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee........eeeeee.....eeeee.hhhhhhhhhhhhhhhhh........................eeee....eeee...hhhhhh....hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhh............hhhhhhhhhhhhhhhhhhhhh.eeeee....ee..hhhhhh....ee...ee..ee..eee.........hhhhhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhh...hhh.eeeee........hhhhhh....eeeee............hhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..............hhhhh...................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhh.............hhhhhhhhhhhhhhhhhhhhhhh-.......hhhhhhhhhhh................hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vcb A  26 GVEITEGVTVTAKGNTEGNTADLAIDGDLSTYWESSNDYKWIEVDLGGIYELSKIEIFNKDEAVYKYNIYASEDGENFNKIAYKNNDNVSDSNGNMHTIDNVRAGKIRIDVVQNSNSDRVNIAEINVFGKNTGESLPE-KKIATSNFSETPWATEYEKFNSDSAYANEKTLNEIKNLVGRVIGREFKDKFIFEIRDQLNGNDVFEVSDSGDGKVLIKGNNGVSLASGFNYYLKNYCNVSYNPIMGSNLKMPETMPSVGERVVIDTPYEHRYALNFCTYSYTMSFWDWDQYEEFLDWCAMNGVNLVLDIIGQEEVLRRTLNEFGYSDEEVKEFISGPAYFAWFYMQNMTGFGGPLPNDWFEQRAELGRKMHDRMQSFGINPVLQGYSGMVPRDFKEKNQEAQTISQGGWCGFDRPDMLKTYVNEGEADYFQKVADVFYEKQKEVFGDVTNFYGVDPFHEGGNTGDLDNGKIYEIIQNKMIEHDNDAVWVIQNWQGNPSNNKLEGLTKKDQAMVLDLFSEVSPDWNRLEERDLPWIWNMLHNFGGRMGMDAAPEKLATEIPKALANSEHMVGIGITPEAINTNPLAYELLFDMAWTRDQINFRTWTEDYIERRYGKTNKEILEAWNIILDTAYKKRNDYYQGAAESIINARPGFGIKSASTWGHSKIVYDKSEFEKAIEIFAKNYDEFKDSDAFLYDFADILKQLLANSAQEYYEVMCNAYNNGNGEKFKFVSGKFLELIKLQERVLSTRPEFLIGNWIEDARTMLKDSDDWTKDLFEFNARALVTTWGSRNNADGGGLKDYSNRQWSGLTEDYYYARWEKWINGLQAELD-GAKAPNIDWFKMEYDWVNKKSDTDKLYPTEASNENLGELAKIAMESYSVTNMDKI 910
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845        |-|      865       875       885       895       905     
                                                                                                                                                                   163 |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              854 |                                                      
                                                                                                                                                                     165                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                856
   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 2VCB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VCB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VCB)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2VCB)

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  Cis Peptide Bonds
    Asn A:520 - Pro A:521   [ RasMol ]  
    Asn A:748 - Gly A:749   [ RasMol ]  
    Gly A:26 - Val A:27   [ RasMol ]  
    Gly A:377 - Pro A:378   [ RasMol ]  
 

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  A0A0H2YU91_C | A0A0H2YU91
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 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2YU91_C | A0A0H2YU91: 2vc9 2vca 2vcc 4a3z 4a6o

(-) Related Entries Specified in the PDB File

2vc9 FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 2-ACETAMIDO-1 ,2-DIDEOXYNOJIRMYCIN
2vca FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH BETA-N-ACETYL -D-GLUCOSAMINE
2vcc FAMILY 89 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRINGENS