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Protein
Submitted name:

Lacto-N-biosidase

Gene

lnbB

Organism
Bifidobacterium bifidum JCM 1254
Status
Unreviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Functioni

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei190 – 1901GalactoseCombined sources
Binding sitei216 – 2161GalactoseCombined sources
Binding sitei259 – 2591GalactoseCombined sources
Binding sitei320 – 3201GalactoseCombined sources
Binding sitei394 – 3941N-acetyl-D-glucosamineCombined sources
Binding sitei419 – 4191N-acetyl-D-glucosamineCombined sources

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

GlycosidaseImported, Hydrolase

Enzyme and pathway databases

BRENDAi3.2.1.140. 844.

Protein family/group databases

CAZyiCBM32. Carbohydrate-Binding Module Family 32.
GH20. Glycoside Hydrolase Family 20.

Names & Taxonomyi

Protein namesi
Submitted name:
Lacto-N-biosidaseImported (EC:3.2.1.140Imported)
Gene namesi
Name:lnbBImported
OrganismiBifidobacterium bifidum JCM 1254Imported
Taxonomic identifieri398514 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaBifidobacterialesBifidobacteriaceaeBifidobacterium

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei1087 – 110620HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3434Sequence analysisAdd
BLAST
Chaini35 – 11121078Sequence analysisPRO_5002799108Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi187 ↔ 189Combined sources
Disulfide bondi564 ↔ 589Combined sources

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H04X-ray1.80A/B41-663[»]
4JAWX-ray1.80A/B41-663[»]
5BXPX-ray1.70A/B41-663[»]
5BXRX-ray1.60A/B41-663[»]
5BXSX-ray2.20A/B41-663[»]
5BXTX-ray1.80A/B41-663[»]
ProteinModelPortaliB3TLD6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini960 – 104182BID_2InterPro annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni320 – 3212N-acetyl-D-glucosamine bindingCombined sources
Regioni465 – 4673Galactose bindingCombined sources
Regioni465 – 4673N-acetyl-D-glucosamine bindingCombined sources

Keywords - Domaini

SignalSequence analysis, Transmembrane, Transmembrane helixSequence analysis

Family and domain databases

Gene3Di2.60.120.260. 1 hit.
3.20.20.80. 1 hit.
3.30.379.10. 1 hit.
InterProiIPR025705. Beta_hexosaminidase_sua/sub.
IPR003343. Big_2.
IPR029018. Chitobiase/Hex_dom_2-like.
IPR000421. FA58C.
IPR008979. Galactose-bd-like.
IPR015883. Glyco_hydro_20_cat.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
IPR015882. HEX_bac_N.
IPR008964. Invasin/intimin_cell_adhesion.
IPR000772. Ricin_B_lectin.
[Graphical view]
PfamiPF02368. Big_2. 1 hit.
PF00754. F5_F8_type_C. 1 hit.
PF00728. Glyco_hydro_20. 1 hit.
PF02838. Glyco_hydro_20b. 1 hit.
[Graphical view]
PRINTSiPR00738. GLHYDRLASE20.
SMARTiSM00635. BID_2. 1 hit.
[Graphical view]
SUPFAMiSSF49373. SSF49373. 1 hit.
SSF49785. SSF49785. 1 hit.
SSF50370. SSF50370. 1 hit.
SSF51445. SSF51445. 1 hit.
SSF55545. SSF55545. 1 hit.

Sequencei

Sequence statusi: Complete.

B3TLD6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKSSNRRFG VRTVAAIVAG LMVGGMCTAM TASAADDSAA GYSATAPVNL
60 70 80 90 100
TRPATVPSMD GWTDGTGAWT LGEGTRVVSS DALAARAQSL ASELTKFTDV
110 120 130 140 150
DIKAATGSAT GKDISLTLDA SKKAELGDEG FKLNIGSKGL EVIGATDIGV
160 170 180 190 200
FYGTRSVSQM LRQGQLTLPA GTVATKPKYK ERGATLCACQ INISTDWIDR
210 220 230 240 250
FLSDMADLRL NYVLLEMKLK PEEDNTKKAA TWSYYTRDDV KKFVKKANNY
260 270 280 290 300
GIDVIPEINS PGHMNVWLEN YPEYQLADNS GRKDPNKLDI SNPEAVKFYK
310 320 330 340 350
TLIDEYDGVF TTKYWHMGAD EYMIGTSFDN YSKLKTFAEK QYGAGATPND
360 370 380 390 400
AFTGFINDID KYVKAKGKQL RIWNDGIVNT KNVSLNKDIV IEYWYGAGRK
410 420 430 440 450
PQELVQDGYT LMNATQALYW SRSAQVYKVN AARLYNNNWN VGTFDGGRQI
460 470 480 490 500
DKNYDKLTGA KVSIWPDSSY FQTENEVEKE IFDGMRFISQ MTWSDSRPWA
510 520 530 540 550
TWNDMKADID KIGYPLDIRE YDYTPVDAGI YDIPQLKSIS KGPWELITTP
560 570 580 590 600
DGYYQMKDTV SGKCLALFTG SKHLDVVTQV GARPELRNCA DVSVGQDQRN
610 620 630 640 650
TANERNTQKW QIRADKDGKY TISPALTQQR LAIATGNEQN IDLETHRPAA
660 670 680 690 700
GTVAQFPADL VSDNALFTLT GHMGMSATVD SKTVNPASPS KITVKVRAAS
710 720 730 740 750
NANTGDVTVT PVVPEGWEIK PGSVSLKSIP AGKAAIAYFN VVNTTGTGDA
760 770 780 790 800
TVQFKLTNTK TGEELGTTSV ALTGSLTKDV EASDYAASSQ ETTGEHAPVG
810 820 830 840 850
NAFDKNANTF WHSKYSNPSA NLPHWLAFKA SPGEGNKIAA ITHLYRQDKL
860 870 880 890 900
NGPAKNVAVY VVAASDANSV ADVTNWGEPV ATAEFPYTKE LQTIALPNTI
910 920 930 940 950
PSGDVYVKFQ INDAWGLTET SAGVTWAAVA ELAATAKATP VELTEPEQPK
960 970 980 990 1000
DNPEVTETPE ATGVTVSGDG VANGALSLKK GTTAQLTAKV APDDADQAVT
1010 1020 1030 1040 1050
WASSDDKVVT VDKTGKVTAV AKGVAKVTAT TANGKSASVT VTVTEDSEVP
1060 1070 1080 1090 1100
GPTGPTEPTK PGTEKPTTKP TTKPNDGKLS ATGADTAVLA TIAALFALAG
1110
GAVVAVRRRS VR
Length:1,112
Mass (Da):119,514
Last modified:September 2, 2008 - v1
Checksum:iBD036BDCD27451F0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU281545 Genomic DNA. Translation: ABZ78855.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU281545 Genomic DNA. Translation: ABZ78855.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4H04X-ray1.80A/B41-663[»]
4JAWX-ray1.80A/B41-663[»]
5BXPX-ray1.70A/B41-663[»]
5BXRX-ray1.60A/B41-663[»]
5BXSX-ray2.20A/B41-663[»]
5BXTX-ray1.80A/B41-663[»]
ProteinModelPortaliB3TLD6.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

CAZyiCBM32. Carbohydrate-Binding Module Family 32.
GH20. Glycoside Hydrolase Family 20.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi3.2.1.140. 844.

Family and domain databases

Gene3Di2.60.120.260. 1 hit.
3.20.20.80. 1 hit.
3.30.379.10. 1 hit.
InterProiIPR025705. Beta_hexosaminidase_sua/sub.
IPR003343. Big_2.
IPR029018. Chitobiase/Hex_dom_2-like.
IPR000421. FA58C.
IPR008979. Galactose-bd-like.
IPR015883. Glyco_hydro_20_cat.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
IPR015882. HEX_bac_N.
IPR008964. Invasin/intimin_cell_adhesion.
IPR000772. Ricin_B_lectin.
[Graphical view]
PfamiPF02368. Big_2. 1 hit.
PF00754. F5_F8_type_C. 1 hit.
PF00728. Glyco_hydro_20. 1 hit.
PF02838. Glyco_hydro_20b. 1 hit.
[Graphical view]
PRINTSiPR00738. GLHYDRLASE20.
SMARTiSM00635. BID_2. 1 hit.
[Graphical view]
SUPFAMiSSF49373. SSF49373. 1 hit.
SSF49785. SSF49785. 1 hit.
SSF50370. SSF50370. 1 hit.
SSF51445. SSF51445. 1 hit.
SSF55545. SSF55545. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure."
    Wada J., Ando T., Kiyohara M., Ashida H., Kitaoka M., Yamaguchi M., Kumagai H., Katayama T., Yamamoto K.
    Appl. Environ. Microbiol. 74:3996-4004(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: JCM 1254Imported.
  2. "Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum."
    Ito T., Katayama T., Hattie M., Sakurama H., Wada J., Suzuki R., Ashida H., Wakagi T., Yamamoto K., Stubbs K.A., Fushinobu S.
    J. Biol. Chem. 288:11795-11806(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 41-663 IN COMPLEX WITH GALACTOSE AND N-ACETYL-D-GLUCOSAMINE, DISULFIDE BONDS.
  3. "Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis."
    Hattie M., Ito T., Debowski A.W., Arakawa T., Katayama T., Yamamoto K., Fushinobu S., Stubbs K.A.
    Chem. Commun. (Camb.) 51:15008-15011(2015) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 41-663, DISULFIDE BONDS.

Entry informationi

Entry nameiB3TLD6_BIFBI
AccessioniPrimary (citable) accession number: B3TLD6
Entry historyi
Integrated into UniProtKB/TrEMBL: September 2, 2008
Last sequence update: September 2, 2008
Last modified: April 13, 2016
This is version 41 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.