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P40406 (NAGZ_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Beta-hexosaminidase

EC=3.2.1.52
Alternative name(s):
Beta-N-acetylhexosaminidase
N-acetyl-beta-glucosaminidase
N-acetylglucosaminidase
ORF1
Gene names
Name:nagZ
Synonyms:ybbD, yzbA
Ordered Locus Names:BSU01660
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length642 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.5

Catalytic activity

Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. Ref.4 Ref.5

Pathway

Cell wall biogenesis; peptidoglycan recycling.

Subcellular location

Cell membrane; Lipid-anchor Potential. Secretedcell wall. Note: Detected in the culture supernatant, predominantly associated with cell wall-derived particulate material. A minor proportion is detected in the soluble fraction. Ref.4

Induction

Up-regulated during the late phase of exponential growth and during stationary phase. Ref.4

Sequence similarities

Belongs to the glycosyl hydrolase 3 family.

Biophysicochemical properties

pH dependence:

Optimum pH is 5.8-6.2. Ref.5

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1616 Potential
Chain17 – 642626Beta-hexosaminidase
PRO_0000011785

Regions

Region221 – 2222Substrate binding

Sites

Active site2341Proton donor/acceptor Ref.5 Ref.6
Active site3181Nucleophile Ref.5 Ref.6
Binding site1231Substrate
Binding site1311Substrate
Binding site1911Substrate
Site2321Important for catalytic activity

Amino acid modifications

Lipidation171N-palmitoyl cysteine Potential
Lipidation171S-diacylglycerol cysteine Potential

Experimental info

Mutagenesis2321D → G: Strongly reduces catalytic efficiency and enzyme activity. Slightly increases substrate affinity. Ref.5
Mutagenesis2341H → G: Strongly reduces catalytic efficiency while increasing substrate affinity. Ref.5
Mutagenesis3181D → N: Abolishes enzyme activity. Ref.6

Secondary structure

........................................................................................................... 642
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P40406 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: DCEA93142922F13F

FASTA64270,580
        10         20         30         40         50         60 
MRPVFPLILS AVLFLSCFFG ARQTEASASK RAIDANQIVN RMSLDEKLGQ MLMPDFRNWQ 

        70         80         90        100        110        120 
KEGESSPQAL TKMNDEVASL VKKYQFGGII LFAENVKTTK QTVQLTDDYQ KASPKIPLML 

       130        140        150        160        170        180 
SIDQEGGIVT RLGEGTNFPG NMALGAARSR INAYQTGSII GKELSALGIN TDFSPVVDIN 

       190        200        210        220        230        240 
NNPDNPVIGV RSFSSNRELT SRLGLYTMKG LQRQDIASAL KHFPGHGDTD VDSHYGLPLV 

       250        260        270        280        290        300 
SHGQERLREV ELYPFQKAID AGADMVMTAH VQFPAFDDTT YKSKLDGSDI LVPATLSKKV 

       310        320        330        340        350        360 
MTGLLRQEMG FNGVIVTDAL NMKAIADHFG QEEAVVMAVK AGVDIALMPA SVTSLKEEQK 

       370        380        390        400        410        420 
FARVIQALKE AVKNGDIPEQ QINNSVERII SLKIKRGMYP ARNSDSTKEK IAKAKKIVGS 

       430        440        450        460        470        480 
KQHLKAEKKL AEKAVTVLKN EQHTLPFKPK KGSRILIVAP YEEQTASIEQ TIHDLIKRKK 

       490        500        510        520        530        540 
IKPVSLSKMN FASQVFKTEH EKQVKEADYI ITGSYVVKND PVVNDGVIDD TISDSSKWAT 

       550        560        570        580        590        600 
VFPRAVMKAA LQHNKPFVLM SLRNPYDAAN FEEAKALIAV YGFKGYANGR YLQPNIPAGV 

       610        620        630        640 
MAIFGQAKPK GTLPVDIPSV TKPGNTLYPL GYGLNIKTGR PL 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L19954 Genomic DNA. Translation: AAA64351.1.
AB002150 Genomic DNA. Translation: BAA19499.1.
AL009126 Genomic DNA. Translation: CAB11942.1.
PIRI39839.
RefSeqNP_388047.1. NC_000964.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP40406.
SMRP40406. Positions 26-642.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU01660.

Protein family/group databases

CAZyGH3. Glycoside Hydrolase Family 3.

Proteomic databases

PaxDbP40406.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB11942; CAB11942; BSU01660.
GeneID938881.
KEGGbsu:BSU01660.
PATRIC18971875. VBIBacSub10457_0171.

Organism-specific databases

GenoListBSU01660. [Micado]

Phylogenomic databases

eggNOGCOG1472.
HOGENOMHOG000248527.
KOK01207.
OMAGQMLMPD.
OrthoDBEOG6X9MKR.
PhylomeDBP40406.

Enzyme and pathway databases

BioCycBSUB:BSU01660-MONOMER.
UniPathwayUPA00544.

Family and domain databases

Gene3D3.20.20.300. 1 hit.
3.40.50.1700. 1 hit.
InterProIPR019800. Glyco_hydro_3_AS.
IPR002772. Glyco_hydro_3_C.
IPR001764. Glyco_hydro_3_N.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PfamPF00933. Glyco_hydro_3. 1 hit.
PF01915. Glyco_hydro_3_C. 1 hit.
[Graphical view]
SUPFAMSSF51445. SSF51445. 1 hit.
SSF52279. SSF52279. 1 hit.
PROSITEPS00775. GLYCOSYL_HYDROL_F3. 1 hit.
PS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP40406.

Entry information

Entry nameNAGZ_BACSU
AccessionPrimary (citable) accession number: P40406
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 9, 2014
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList