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P40406

- NAGZ_BACSU

UniProt

P40406 - NAGZ_BACSU

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Protein

Beta-hexosaminidase

Gene

nagZ

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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. cell wall organization Source: UniProtKB-KW
  3. peptidoglycan biosynthetic process Source: UniProtKB-KW
  4. peptidoglycan turnover Source: UniProtKB-UniPathway
  5. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

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-KW
  2. extracellular region Source: UniProtKB-KW
  3. plasma membrane Source: UniProtKB-KW
Complete GO annotation...

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.
InParanoidiP40406.
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

        10         20         30         40         50
MRPVFPLILS AVLFLSCFFG ARQTEASASK RAIDANQIVN RMSLDEKLGQ
60 70 80 90 100
MLMPDFRNWQ KEGESSPQAL TKMNDEVASL VKKYQFGGII LFAENVKTTK
110 120 130 140 150
QTVQLTDDYQ KASPKIPLML SIDQEGGIVT RLGEGTNFPG NMALGAARSR
160 170 180 190 200
INAYQTGSII GKELSALGIN TDFSPVVDIN NNPDNPVIGV RSFSSNRELT
210 220 230 240 250
SRLGLYTMKG LQRQDIASAL KHFPGHGDTD VDSHYGLPLV SHGQERLREV
260 270 280 290 300
ELYPFQKAID AGADMVMTAH VQFPAFDDTT YKSKLDGSDI LVPATLSKKV
310 320 330 340 350
MTGLLRQEMG FNGVIVTDAL NMKAIADHFG QEEAVVMAVK AGVDIALMPA
360 370 380 390 400
SVTSLKEEQK FARVIQALKE AVKNGDIPEQ QINNSVERII SLKIKRGMYP
410 420 430 440 450
ARNSDSTKEK IAKAKKIVGS KQHLKAEKKL AEKAVTVLKN EQHTLPFKPK
460 470 480 490 500
KGSRILIVAP YEEQTASIEQ TIHDLIKRKK IKPVSLSKMN FASQVFKTEH
510 520 530 540 550
EKQVKEADYI ITGSYVVKND PVVNDGVIDD TISDSSKWAT VFPRAVMKAA
560 570 580 590 600
LQHNKPFVLM SLRNPYDAAN FEEAKALIAV YGFKGYANGR YLQPNIPAGV
610 620 630 640
MAIFGQAKPK GTLPVDIPSV TKPGNTLYPL GYGLNIKTGR PL
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.
InParanoidi P40406.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 111 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