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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF DISPERSIN B
 
Authors :  N. Ramasubbu, L. M. Thomas, C. Ragunath, J. B. Kaplan
Date :  10 Jan 05  (Deposition) - 10 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Ramasubbu, L. M. Thomas, C. Ragunath, J. B. Kaplan
Structural Analysis Of Dispersin B, A Biofilm-Releasing Glycoside Hydrolase From The Periodontopathogen Actinobacillus Actinomycetemcomitans.
J. Mol. Biol. V. 349 475 2005
PubMed-ID: 15878175  |  Reference-DOI: 10.1016/J.JMB.2005.03.082
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DSPB
    Chains: A
    EC Number: 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Taxid: 562
    Gene: DSPB
    Organism Scientific: AGGREGATIBACTER ACTINOMYCETEMCOMITANS
    Organism Taxid: 714
    Strain: CU1000

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:183 , TRP A:216 , TRP A:237 , TYR A:278 , GOL A:751BINDING SITE FOR RESIDUE ACY A 750
2AC2SOFTWAREARG A:27 , GLU A:332 , HOH A:450 , HOH A:628 , HOH A:629 , ACY A:750BINDING SITE FOR RESIDUE GOL A 751
3AC3SOFTWARESER A:165 , GLU A:166 , ASP A:169 , ILE A:170 , LYS A:209 , HOH A:406 , HOH A:638BINDING SITE FOR RESIDUE GOL A 752

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YHT)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:117 -Pro A:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YHT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YHT)

(-) Exons   (0, 0)

(no "Exon" information available for 1YHT)

(-) 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:344
 aligned with Q840G9_AGGAC | Q840G9 from UniProtKB/TrEMBL  Length:361

    Alignment length:344
                                    25        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    
         Q840G9_AGGAC    16 TKQTGLMLDIARHFYSPEVIKSFIDTISLSGGNFLHLHFSDHENYAIESHLLNQRAENAVQGKDGIYINPYTGKPFLSYRQLDDIKAYAKAKGIELIPELDSPNHMTAIFKLVQKDRGVKYLQGLKSRQVDDEIDITNADSITFMQSLMSEVIDIFGDTSQHFHIGGDEFGYSVESNHEFITYANKLSYFLEKKGLKTRMWNDGLIKNTFEQINPNIEITYWSYDGDTQDKNEAAERRDMRVSLPELLAKGFTVLNYNSYYLYIVPKASPTFSQDAAFAAKDVIKNWDLGVWDGRNTKNRVQNTHEIAGAALSIWGEDAKALKDETIQKNTKSLLEAVIHKTNG 359
               SCOP domains d1yhta1 A:16-359 Dispersin B, DspB                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhhh...eeeee................hhhhhee.....ee......ee.hhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhh....eeee........hhhhhhhhhhhh.hhhhhhhh...eee.hhhhhee......hhhhhhhhhhhhhhhhh...............hhhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yht A  16 TKQTGLMLDIARHFYSPEVIKSFIDTISLSGGNFLHLHFSDHENYAIESHLLNQRAENAVQGKDGIYINPYTGKPFLSYRQLDDIKAYAKAKGIELIPELDSPNHMTAIFKLVQKDRGVKYLQGLKSRQVDDEIDITNADSITFMQSLMSEVIDIFGDTSQHFHIGGDEFGYSVESNHEFITYANKLSYFLEKKGLKTRMWNDGLIKNTFEQINPNIEITYWSYDGDTQDKNEAAERRDMRVSLPELLAKGFTVLNYNSYYLYIVPKASPTFSQDAAFAAKDVIKNWDLGVWDGRNTKNRVQNTHEIAGAALSIWGEDAKALKDETIQKNTKSLLEAVIHKTNG 359
                                    25        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
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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YHT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YHT)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q840G9_AGGAC | Q840G9)
molecular function
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1hp4 SAME FAMILY 20 ENZYME
1now SAME FAMILY 20 ENZYME
1o7a SAME FAMILY 20 ENZYME
1qbb SAME FAMILY 20 ENZYME