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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)DescriptionActionsGraphical viewLength
Active sitei76Acyl-ester intermediatePROSITE-ProRule annotation1

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)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Sequence analysisAdd BLAST23
ChainiPRO_000001704924 – 267Probable beta-lactamase YbxIAdd BLAST244

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei79N6-carboxylysineBy similarity1

Proteomic databases

PaxDbiP54427.

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100001168.

Structurei

Secondary structure

1267
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi34 – 36Combined sources3
Helixi40 – 43Combined sources4
Beta strandi48 – 54Combined sources7
Turni55 – 58Combined sources4
Beta strandi59 – 64Combined sources6
Helixi65 – 68Combined sources4
Helixi75 – 77Combined sources3
Helixi78 – 88Combined sources11
Helixi109 – 111Combined sources3
Helixi117 – 122Combined sources6
Helixi126 – 136Combined sources11
Helixi138 – 147Combined sources10
Turni159 – 163Combined sources5
Beta strandi164 – 167Combined sources4
Helixi172 – 183Combined sources12
Beta strandi187 – 189Combined sources3
Helixi191 – 200Combined sources10
Beta strandi202 – 205Combined sources4
Beta strandi207 – 217Combined sources11
Turni219 – 222Combined sources4
Beta strandi225 – 233Combined sources9
Beta strandi236 – 246Combined sources11
Helixi248 – 261Combined sources14

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni214 – 216Substrate bindingBy similarity3

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)DescriptionActionsGraphical viewLength
Sequence conflicti129 – 137YQALARDIG → IISISERYR (PubMed:9016963).Curated9
Sequence conflicti169T → A in CAA63445 (PubMed:9016963).Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5E2FX-ray1.30A/B1-267[»]
ProteinModelPortaliP54427.
SMRiP54427.
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: November 2, 2016
This is version 112 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.