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(-) Description

Title :  STRUCTURE OF BETA-HEXOSAMINIDASE FROM VIBRIO CHOLERAE
 
Authors :  J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  21 Jun 04  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha Barrel, Beta-Hexosaminidase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Gorman, L. Shapiro
Structure Of Beta-Hexosaminidase From Vibrio Cholerae
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-HEXOSAMINIDASE
    ChainsA
    EC Number3.2.1.52
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidMODIFIED PET26B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneNAMENAGZ;
ORDEREDLOCUSNAMES
VC0692
    Organism ScientificVIBRIO CHOLERAE
    Organism Taxid666
    SynonymN-ACETYL-BETA-GLUCOSAMINIDASE, BETA-N- ACETYLHEXOSAMINIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1TR9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TR9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:115 -Pro A:116
2Lys A:160 -His A:161
3Phe A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TR9)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F3PS00775 Glycosyl hydrolases family 3 active site.NAGZ_VIBCH228-245  1A:228-245

(-) Exons   (0, 0)

(no "Exon" information available for 1TR9)

(-) 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:330
 aligned with NAGZ_VIBCH | Q9KU37 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:330
                             1                                                                                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329
           NAGZ_VIBCH     - -MGPLWLDVAGYELSAEDREILQHPTVGGVILFGRNYHDNQQLLALNKAIRQAAKRPILIGVDQEGGRVQRFREGFSRIPPAQYYARAENGVELAEQGGWLMAAELIAHDVDLSFAPVLDMGFACKAIGNRAFGEDVQTVLKHSSAFLRGMKAVGMATTGKHFPGHGAVIADSHLETPYDERETIAQDMAIFRAQIEAGVLDAMMPAHVVYPHYDAQPASGSSYWLKQVLREELGFKGIVFSDDLSMEGAAVMGGPVERSHQALVAGCDMILICNKREAAVEVLDNLPIMEVPQAEALLKKQQFSYSELKRLERWQQASANMQRLIEQFS 329
               SCOP domains d1tr9a_ A: Beta-hexosaminidase NagZ                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1tr9A00 A:0-329  [code=3.20.20.300, no name defined]                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -----Glyco_hydro_3-1tr9A01 A:5-310                                                                                                                                                                                                                                                                                     ------------------- Pfam domains
         Sec.struct. author ....eee.......hhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhhhhh...eeee.eee..ee..........hhhhhhhh.hhhhhhhhhhhhhhhhhhh....ee.............hhhhh...hhhhhhhhhhhhhhhhhhh....eeeee.....................hhhhhhhhhhhhhhh...eeee...........hhhhhhhhhh...........eeeeee..........hhhhhhhhhhhhh..eee...hhhhhhhhhhhh....hhhhhhhh.....hhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F3------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tr9 A   0 SLGPLWLDVAGYELSAEDREILQHPTVGGVILFGRNYHDNQQLLALNKAIRQAAKRPILIGVDQEGGRVQRFREGFSRIPPAQYYARAENGVELAEQGGWLmAAELIAHDVDLSFAPVLDmGFACKAIGNRAFGEDVQTVLKHSSAFLRGmKAVGmATTGKHFPGHGAVIADSHLETPYDERETIAQDmAIFRAQIEAGVLDAmmPAHVVYPHYDAQPASGSSYWLKQVLREELGFKGIVFSDDLSmEGAAVmGGPVERSHQALVAGCDmILICNKREAAVEVLDNLPImEVPQAEALLKKQQFSYSELKRLERWQQASANmQRLIEQFS 329
                                     9        19        29        39        49        59        69        79        89        99 |     109       119|      129       139       149|    | 159       169       179       189       199   ||  209       219       229       239      |249  |    259       269       279       289       299       309       319 |     329
                                                                                                                               101-MSE            120-MSE                       150-MSE|                              188-MSE        203-MSE                                    246-MSE |              269-MSE             289-MSE                         321-MSE    
                                                                                                                                                                                     155-MSE                                          204-MSE                                         252-MSE                                                                         

   Legend:   → Mismatch (orange background)
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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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NAGZ_VIBCH | Q9KU37)
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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    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.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
    GO:0009273    peptidoglycan-based cell wall biogenesis    The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Cis Peptide Bonds
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 Related Entries

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UniProtKB/Swiss-Prot
        NAGZ_VIBCH | Q9KU371y65 2oxn 3gs6 3gsm

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