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P40406

- NAGZ_BACSU

UniProt

P40406 - NAGZ_BACSU

Protein

Beta-hexosaminidase

Gene

nagZ

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 110 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Plays a role in peptidoglycan recycling by cleaving the terminal beta-1,4-linked N-acetylglucosamine (GlcNAc) from peptide-linked peptidoglycan fragments, giving rise to free GlcNAc, anhydro-N-acetylmuramic acid and anhydro-N-acetylmuramic acid-linked peptides. Cleaves muropeptides, but not peptidoglycan.2 Publications

    Catalytic activityi

    Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.2 Publications

    pH dependencei

    Optimum pH is 5.8-6.2.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei123 – 1231Substrate
    Binding sitei131 – 1311Substrate
    Binding sitei191 – 1911Substrate
    Sitei232 – 2321Important for catalytic activity
    Active sitei234 – 2341Proton donor/acceptor
    Active sitei318 – 3181Nucleophile

    GO - Molecular functioni

    1. beta-N-acetylhexosaminidase activity Source: UniProtKB-EC

    GO - Biological processi

    1. carbohydrate metabolic process Source: InterPro
    2. peptidoglycan biosynthetic process Source: UniProtKB-KW
    3. peptidoglycan turnover Source: UniProtKB-UniPathway
    4. regulation of cell shape Source: UniProtKB-KW

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Enzyme and pathway databases

    BioCyciBSUB:BSU01660-MONOMER.
    UniPathwayiUPA00544.

    Protein family/group databases

    CAZyiGH3. Glycoside Hydrolase Family 3.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Beta-hexosaminidase (EC:3.2.1.52)
    Alternative name(s):
    Beta-N-acetylhexosaminidase
    N-acetyl-beta-glucosaminidase
    N-acetylglucosaminidase
    ORF1
    Gene namesi
    Name:nagZ
    Synonyms:ybbD, yzbA
    Ordered Locus Names:BSU01660
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001570: Chromosome

    Organism-specific databases

    GenoListiBSU01660. [Micado]

    Subcellular locationi

    Cell membrane PROSITE-ProRule annotation; Lipid-anchor PROSITE-ProRule annotation. Secretedcell wall 1 Publication
    Note: Detected in the culture supernatant, predominantly associated with cell wall-derived particulate material. A minor proportion is detected in the soluble fraction.

    GO - Cellular componenti

    1. cell wall Source: UniProtKB-SubCell
    2. extracellular region Source: UniProtKB-KW
    3. plasma membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell membrane, Cell wall, Membrane, Secreted

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi232 – 2321D → G: Strongly reduces catalytic efficiency and enzyme activity. Slightly increases substrate affinity. 1 Publication
    Mutagenesisi234 – 2341H → G: Strongly reduces catalytic efficiency while increasing substrate affinity. 1 Publication
    Mutagenesisi318 – 3181D → N: Abolishes enzyme activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 1616PROSITE-ProRule annotationAdd
    BLAST
    Chaini17 – 642626Beta-hexosaminidasePRO_0000011785Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi17 – 171N-palmitoyl cysteinePROSITE-ProRule annotation
    Lipidationi17 – 171S-diacylglycerol cysteinePROSITE-ProRule annotation

    Keywords - PTMi

    Lipoprotein, Palmitate

    Proteomic databases

    PaxDbiP40406.

    Expressioni

    Inductioni

    Up-regulated during the late phase of exponential growth and during stationary phase.1 Publication

    Interactioni

    Protein-protein interaction databases

    STRINGi224308.BSU01660.

    Structurei

    Secondary structure

    1
    642
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi27 – 4014
    Helixi44 – 507
    Beta strandi57 – 593
    Helixi75 – 8410
    Beta strandi87 – 904
    Helixi93 – 953
    Helixi99 – 11214
    Beta strandi114 – 1163
    Beta strandi119 – 1224
    Beta strandi133 – 1353
    Helixi141 – 1477
    Helixi150 – 16718
    Beta strandi186 – 1883
    Helixi189 – 1913
    Helixi197 – 21317
    Beta strandi217 – 2237
    Helixi226 – 2283
    Beta strandi230 – 2323
    Turni233 – 2353
    Beta strandi237 – 2393
    Helixi244 – 2496
    Helixi252 – 2609
    Beta strandi265 – 2684
    Turni274 – 2763
    Beta strandi280 – 2823
    Turni284 – 2863
    Beta strandi289 – 2913
    Helixi294 – 2963
    Helixi298 – 3014
    Helixi302 – 3087
    Beta strandi313 – 3164
    Helixi323 – 3264
    Helixi331 – 34111
    Beta strandi344 – 3485
    Helixi355 – 3584
    Helixi359 – 37315
    Helixi379 – 39517
    Turni396 – 4016
    Helixi407 – 41711
    Helixi421 – 43414
    Beta strandi436 – 4405
    Helixi441 – 4433
    Beta strandi454 – 4618
    Helixi462 – 47716
    Beta strandi485 – 4906
    Helixi498 – 5069
    Beta strandi508 – 5147
    Helixi535 – 5373
    Helixi538 – 55215
    Beta strandi557 – 5615
    Helixi565 – 5706
    Beta strandi575 – 5795
    Beta strandi590 – 5923
    Helixi595 – 6039
    Beta strandi620 – 6223
    Beta strandi625 – 6284
    Turni636 – 6383

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3BMXX-ray1.40A/B1-642[»]
    3LK6X-ray2.88A/B/C/D27-642[»]
    3NVDX-ray1.70A/B1-642[»]
    4GYJX-ray1.65A/B18-642[»]
    4GYKX-ray1.80A/B18-642[»]
    ProteinModelPortaliP40406.
    SMRiP40406. Positions 26-642.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40406.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni221 – 2222Substrate binding

    Sequence similaritiesi

    Belongs to the glycosyl hydrolase 3 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiCOG1472.
    HOGENOMiHOG000248527.
    KOiK01207.
    OMAiGQMLMPD.
    OrthoDBiEOG6X9MKR.
    PhylomeDBiP40406.

    Family and domain databases

    Gene3Di3.20.20.300. 1 hit.
    3.40.50.1700. 1 hit.
    InterProiIPR019800. Glyco_hydro_3_AS.
    IPR002772. Glyco_hydro_3_C.
    IPR001764. Glyco_hydro_3_N.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view]
    PfamiPF00933. Glyco_hydro_3. 1 hit.
    PF01915. Glyco_hydro_3_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF51445. SSF51445. 1 hit.
    SSF52279. SSF52279. 1 hit.
    PROSITEiPS00775. GLYCOSYL_HYDROL_F3. 1 hit.
    PS51257. PROKAR_LIPOPROTEIN. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P40406-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRPVFPLILS AVLFLSCFFG ARQTEASASK RAIDANQIVN RMSLDEKLGQ    50
    MLMPDFRNWQ KEGESSPQAL TKMNDEVASL VKKYQFGGII LFAENVKTTK 100
    QTVQLTDDYQ KASPKIPLML SIDQEGGIVT RLGEGTNFPG NMALGAARSR 150
    INAYQTGSII GKELSALGIN TDFSPVVDIN NNPDNPVIGV RSFSSNRELT 200
    SRLGLYTMKG LQRQDIASAL KHFPGHGDTD VDSHYGLPLV SHGQERLREV 250
    ELYPFQKAID AGADMVMTAH VQFPAFDDTT YKSKLDGSDI LVPATLSKKV 300
    MTGLLRQEMG FNGVIVTDAL NMKAIADHFG QEEAVVMAVK AGVDIALMPA 350
    SVTSLKEEQK FARVIQALKE AVKNGDIPEQ QINNSVERII SLKIKRGMYP 400
    ARNSDSTKEK IAKAKKIVGS KQHLKAEKKL AEKAVTVLKN EQHTLPFKPK 450
    KGSRILIVAP YEEQTASIEQ TIHDLIKRKK IKPVSLSKMN FASQVFKTEH 500
    EKQVKEADYI ITGSYVVKND PVVNDGVIDD TISDSSKWAT VFPRAVMKAA 550
    LQHNKPFVLM SLRNPYDAAN FEEAKALIAV YGFKGYANGR YLQPNIPAGV 600
    MAIFGQAKPK GTLPVDIPSV TKPGNTLYPL GYGLNIKTGR PL 642
    Length:642
    Mass (Da):70,580
    Last modified:February 1, 1995 - v1
    Checksum:iDCEA93142922F13F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L19954 Genomic DNA. Translation: AAA64351.1.
    AB002150 Genomic DNA. Translation: BAA19499.1.
    AL009126 Genomic DNA. Translation: CAB11942.1.
    PIRiI39839.
    RefSeqiNP_388047.1. NC_000964.3.
    WP_003234975.1. NZ_CM000487.1.

    Genome annotation databases

    EnsemblBacteriaiCAB11942; CAB11942; BSU01660.
    GeneIDi938881.
    KEGGibsu:BSU01660.
    PATRICi18971875. VBIBacSub10457_0171.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L19954 Genomic DNA. Translation: AAA64351.1 .
    AB002150 Genomic DNA. Translation: BAA19499.1 .
    AL009126 Genomic DNA. Translation: CAB11942.1 .
    PIRi I39839.
    RefSeqi NP_388047.1. NC_000964.3.
    WP_003234975.1. NZ_CM000487.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3BMX X-ray 1.40 A/B 1-642 [» ]
    3LK6 X-ray 2.88 A/B/C/D 27-642 [» ]
    3NVD X-ray 1.70 A/B 1-642 [» ]
    4GYJ X-ray 1.65 A/B 18-642 [» ]
    4GYK X-ray 1.80 A/B 18-642 [» ]
    ProteinModelPortali P40406.
    SMRi P40406. Positions 26-642.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 224308.BSU01660.

    Protein family/group databases

    CAZyi GH3. Glycoside Hydrolase Family 3.

    Proteomic databases

    PaxDbi P40406.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAB11942 ; CAB11942 ; BSU01660 .
    GeneIDi 938881.
    KEGGi bsu:BSU01660.
    PATRICi 18971875. VBIBacSub10457_0171.

    Organism-specific databases

    GenoListi BSU01660. [Micado ]

    Phylogenomic databases

    eggNOGi COG1472.
    HOGENOMi HOG000248527.
    KOi K01207.
    OMAi GQMLMPD.
    OrthoDBi EOG6X9MKR.
    PhylomeDBi P40406.

    Enzyme and pathway databases

    UniPathwayi UPA00544 .
    BioCyci BSUB:BSU01660-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P40406.

    Family and domain databases

    Gene3Di 3.20.20.300. 1 hit.
    3.40.50.1700. 1 hit.
    InterProi IPR019800. Glyco_hydro_3_AS.
    IPR002772. Glyco_hydro_3_C.
    IPR001764. Glyco_hydro_3_N.
    IPR017853. Glycoside_hydrolase_SF.
    [Graphical view ]
    Pfami PF00933. Glyco_hydro_3. 1 hit.
    PF01915. Glyco_hydro_3_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51445. SSF51445. 1 hit.
    SSF52279. SSF52279. 1 hit.
    PROSITEi PS00775. GLYCOSYL_HYDROL_F3. 1 hit.
    PS51257. PROKAR_LIPOPROTEIN. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Isolation of Tn917 insertional mutants of Bacillus subtilis that are resistant to the protonophore carbonyl cyanide m-chlorophenylhydrazone."
      Quirk P.G., Guffanti A.A., Clejan S., Cheng J., Krulwich T.A.
      Biochim. Biophys. Acta 1186:27-34(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: BD99 / MS94.
    2. "Sequence and analysis of a 31 kb segment of the Bacillus subtilis chromosome in the area of the rrnH and rrnG operons."
      Liu H., Haga K., Yasumoto K., Ohashi Y., Yoshikawa H., Takahashi H.
      Microbiology 143:2763-2767(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    3. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    4. "Muropeptide rescue in Bacillus subtilis involves sequential hydrolysis by beta-N-acetylglucosaminidase and N-acetylmuramyl-L-alanine amidase."
      Litzinger S., Duckworth A., Nitzsche K., Risinger C., Wittmann V., Mayer C.
      J. Bacteriol. 192:3132-3143(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, INDUCTION, SUBCELLULAR LOCATION.
      Strain: 168.
    5. "Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism."
      Litzinger S., Fischer S., Polzer P., Diederichs K., Welte W., Mayer C.
      J. Biol. Chem. 285:35675-35684(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) IN COMPLEX WITH TRANSITION STATE ANALOG, CATALYTIC ACTIVITY, FUNCTION, MUTAGENESIS OF ASP-232 AND HIS-234, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: 168.
    6. "Active site plasticity within the glycoside hydrolase NagZ underlies a dynamic mechanism of substrate distortion."
      Bacik J.P., Whitworth G.E., Stubbs K.A., Vocadlo D.J., Mark B.L.
      Chem. Biol. 19:1471-1482(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF 18-642 IN COMPLEX WITH SUBSTRATE ANALOGS, ACTIVE SITE, MUTAGENESIS OF ASP-318.

    Entry informationi

    Entry nameiNAGZ_BACSU
    AccessioniPrimary (citable) accession number: P40406
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 110 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3