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Protein

Probable beta-lactamase YbxI

Gene

ybxI

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

A beta-lactam + H2O = a substituted beta-amino acid.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei76 – 761Acyl-ester intermediatePROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Antibiotic resistance

Enzyme and pathway databases

BioCyciBSUB:BSU02090-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable beta-lactamase YbxI (EC:3.5.2.6)
Gene namesi
Name:ybxI
Synonyms:ybdS
Ordered Locus Names:BSU02090
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2323Sequence analysisAdd
BLAST
Chaini24 – 267244Probable beta-lactamase YbxIPRO_0000017049Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei79 – 791N6-carboxylysineBy similarity

Proteomic databases

PaxDbiP54427.

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100001168.

Structurei

Secondary structure

1
267
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi34 – 363Combined sources
Helixi40 – 434Combined sources
Beta strandi48 – 547Combined sources
Turni55 – 584Combined sources
Beta strandi59 – 646Combined sources
Helixi65 – 684Combined sources
Helixi75 – 773Combined sources
Helixi78 – 8811Combined sources
Helixi109 – 1113Combined sources
Helixi117 – 1226Combined sources
Helixi126 – 13611Combined sources
Helixi138 – 14710Combined sources
Turni159 – 1635Combined sources
Beta strandi164 – 1674Combined sources
Helixi172 – 18312Combined sources
Beta strandi187 – 1893Combined sources
Helixi191 – 20010Combined sources
Beta strandi202 – 2054Combined sources
Beta strandi207 – 21711Combined sources
Turni219 – 2224Combined sources
Beta strandi225 – 2339Combined sources
Beta strandi236 – 24611Combined sources
Helixi248 – 26114Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5E2FX-ray1.30A/B1-267[»]
ProteinModelPortaliP54427.
SMRiP54427. Positions 17-266.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni214 – 2163Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the class-D beta-lactamase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4108HWY. Bacteria.
COG2602. LUCA.
HOGENOMiHOG000296772.
InParanoidiP54427.
KOiK17838.
OMAiWYYQALA.
PhylomeDBiP54427.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR002137. Beta-lactam_class-D_AS.
IPR001460. PCN-bd_Tpept.
[Graphical view]
PfamiPF00905. Transpeptidase. 1 hit.
[Graphical view]
SUPFAMiSSF56601. SSF56601. 1 hit.
PROSITEiPS00337. BETA_LACTAMASE_D. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P54427-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKWIYVVLV LSIAGIGGFS VHAASSAHEK HLNVSKMNVD DEFKDTDGTF
60 70 80 90 100
ILHDLQKDQT FVYNRKRANQ RQTPQSTFKV VNALIGLQVK AVRDEYDVKR
110 120 130 140 150
WDGVKREFES WNRDHTLGSA MRESAIWYYQ ALARDIGEER MKTWLHTLSY
160 170 180 190 200
GNEDISGGID QFWLQSSLTI SPLEQETFLE KLAKEELPFD KPVMKIVKRM
210 220 230 240 250
MIQEEGDHYT LYGKTGTRLT DMGLGWFVGF IKTEHGSYVF VTNVDDSGTK
260
AKNITVDILK KYGLITS
Length:267
Mass (Da):30,644
Last modified:May 30, 2000 - v2
Checksum:iBBE3E698CD46E6ED
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti129 – 1379YQALARDIG → IISISERYR (PubMed:9016963).Curated
Sequence conflicti169 – 1691T → A in CAA63445 (PubMed:9016963).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB006424 Genomic DNA. Translation: BAA33106.1.
AL009126 Genomic DNA. Translation: CAB12003.1.
X92859 Genomic DNA. Translation: CAA63445.1.
PIRiB69752.
RefSeqiNP_388091.1. NC_000964.3.
WP_003246349.1. NZ_JNCM01000030.1.

Genome annotation databases

EnsemblBacteriaiCAB12003; CAB12003; BSU02090.
GeneIDi938466.
KEGGibsu:BSU02090.
PATRICi18971963. VBIBacSub10457_0210.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB006424 Genomic DNA. Translation: BAA33106.1.
AL009126 Genomic DNA. Translation: CAB12003.1.
X92859 Genomic DNA. Translation: CAA63445.1.
PIRiB69752.
RefSeqiNP_388091.1. NC_000964.3.
WP_003246349.1. NZ_JNCM01000030.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5E2FX-ray1.30A/B1-267[»]
ProteinModelPortaliP54427.
SMRiP54427. Positions 17-266.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100001168.

Proteomic databases

PaxDbiP54427.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12003; CAB12003; BSU02090.
GeneIDi938466.
KEGGibsu:BSU02090.
PATRICi18971963. VBIBacSub10457_0210.

Phylogenomic databases

eggNOGiENOG4108HWY. Bacteria.
COG2602. LUCA.
HOGENOMiHOG000296772.
InParanoidiP54427.
KOiK17838.
OMAiWYYQALA.
PhylomeDBiP54427.

Enzyme and pathway databases

BioCyciBSUB:BSU02090-MONOMER.

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR002137. Beta-lactam_class-D_AS.
IPR001460. PCN-bd_Tpept.
[Graphical view]
PfamiPF00905. Transpeptidase. 1 hit.
[Graphical view]
SUPFAMiSSF56601. SSF56601. 1 hit.
PROSITEiPS00337. BETA_LACTAMASE_D. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYBXI_BACSU
AccessioniPrimary (citable) accession number: P54427
Secondary accession number(s): O31439
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: May 30, 2000
Last modified: September 7, 2016
This is version 110 of the entry and version 2 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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.