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Protein

Putative L,D-transpeptidase YkuD

Gene

ykuD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Probable enzyme that may play an important role in cell wall biology.1 Publication

Pathwayi: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosyltransferase, Hydrolase, Transferase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis, Sporulation

Enzyme and pathway databases

BioCyciBSUB:BSU14040-MONOMER.
UniPathwayiUPA00219.

Protein family/group databases

CAZyiCBM50. Carbohydrate-Binding Module Family 50.

Names & Taxonomyi

Protein namesi
Recommended name:
Putative L,D-transpeptidase YkuD (EC:2.-.-.-)
Alternative name(s):
Spore protein YkuD
Gene namesi
Name:ykuD
Ordered Locus Names:BSU14040
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

  • Spore wall 1 Publication

  • Note: Probably localized either on the surface of the outer spore membrane and/or in the inner spore coat.

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002276611 – 164Putative L,D-transpeptidase YkuDAdd BLAST164

Proteomic databases

PaxDbiO34816.

Expressioni

Developmental stagei

Expressed in the mother cell compartment from T4 of sporulation.

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100007796.

Structurei

Secondary structure

1164
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 5Combined sources4
Helixi12 – 18Combined sources7
Helixi23 – 29Combined sources7
Helixi31 – 35Combined sources5
Beta strandi42 – 45Combined sources4
Helixi51 – 53Combined sources3
Beta strandi56 – 61Combined sources6
Turni62 – 65Combined sources4
Beta strandi66 – 71Combined sources6
Beta strandi74 – 80Combined sources7
Beta strandi82 – 84Combined sources3
Helixi86 – 88Combined sources3
Beta strandi93 – 102Combined sources10
Helixi106 – 108Combined sources3
Beta strandi111 – 117Combined sources7
Beta strandi121 – 123Combined sources3
Helixi128 – 130Combined sources3
Beta strandi133 – 141Combined sources9
Helixi144 – 153Combined sources10
Beta strandi159 – 163Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Y7MX-ray2.05A/B1-164[»]
2MTZNMR-A2-164[»]
3ZQDNMR-A2-164[»]
4A1IX-ray1.76A/B/C/D/E/F/G/H1-164[»]
4A1JX-ray2.20A/B1-164[»]
4A1KX-ray1.75A1-164[»]
4A52NMR-A2-164[»]
ProteinModelPortaliO34816.
SMRiO34816.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO34816.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 45LysMPROSITE-ProRule annotationAdd BLAST44

Domaini

LysM domains are thought to be involved in peptidoglycan binding.

Sequence similaritiesi

Belongs to the YkuD family.Curated
Contains 1 LysM domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4107Y2H. Bacteria.
COG1376. LUCA.
HOGENOMiHOG000009616.
InParanoidiO34816.
OMAiKGCIRMH.
PhylomeDBiO34816.

Family and domain databases

CDDicd00118. LysM. 1 hit.
Gene3Di3.10.350.10. 1 hit.
InterProiIPR005490. LD_TPept_cat_dom.
IPR018392. LysM_dom.
[Graphical view]
PfamiPF01476. LysM. 1 hit.
PF03734. YkuD. 1 hit.
[Graphical view]
SMARTiSM00257. LysM. 1 hit.
[Graphical view]
SUPFAMiSSF54106. SSF54106. 1 hit.
PROSITEiPS51782. LYSM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O34816-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLTYQVKQGD TLNSIAADFR ISTAALLQAN PSLQAGLTAG QSIVIPGLPD
60 70 80 90 100
PYTIPYHIAV SIGAKTLTLS LNNRVMKTYP IAVGKILTQT PTGEFYIINR
110 120 130 140 150
QRNPGGPFGA YWLSLSKQHY GIHGTNNPAS IGKAVSKGCI RMHNKDVIEL
160
ASIVPNGTRV TINR
Length:164
Mass (Da):17,643
Last modified:January 1, 1998 - v1
Checksum:i6E13A750890E7F4C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ222587 Genomic DNA. Translation: CAA10867.1.
AL009126 Genomic DNA. Translation: CAB13277.1.
PIRiA69865.
RefSeqiNP_389287.1. NC_000964.3.
WP_010886500.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB13277; CAB13277; BSU14040.
GeneIDi939216.
KEGGibsu:BSU14040.
PATRICi18974593. VBIBacSub10457_1488.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ222587 Genomic DNA. Translation: CAA10867.1.
AL009126 Genomic DNA. Translation: CAB13277.1.
PIRiA69865.
RefSeqiNP_389287.1. NC_000964.3.
WP_010886500.1. NC_000964.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Y7MX-ray2.05A/B1-164[»]
2MTZNMR-A2-164[»]
3ZQDNMR-A2-164[»]
4A1IX-ray1.76A/B/C/D/E/F/G/H1-164[»]
4A1JX-ray2.20A/B1-164[»]
4A1KX-ray1.75A1-164[»]
4A52NMR-A2-164[»]
ProteinModelPortaliO34816.
SMRiO34816.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100007796.

Protein family/group databases

CAZyiCBM50. Carbohydrate-Binding Module Family 50.

Proteomic databases

PaxDbiO34816.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13277; CAB13277; BSU14040.
GeneIDi939216.
KEGGibsu:BSU14040.
PATRICi18974593. VBIBacSub10457_1488.

Phylogenomic databases

eggNOGiENOG4107Y2H. Bacteria.
COG1376. LUCA.
HOGENOMiHOG000009616.
InParanoidiO34816.
OMAiKGCIRMH.
PhylomeDBiO34816.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciBSUB:BSU14040-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO34816.

Family and domain databases

CDDicd00118. LysM. 1 hit.
Gene3Di3.10.350.10. 1 hit.
InterProiIPR005490. LD_TPept_cat_dom.
IPR018392. LysM_dom.
[Graphical view]
PfamiPF01476. LysM. 1 hit.
PF03734. YkuD. 1 hit.
[Graphical view]
SMARTiSM00257. LysM. 1 hit.
[Graphical view]
SUPFAMiSSF54106. SSF54106. 1 hit.
PROSITEiPS51782. LYSM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYKUD_BACSU
AccessioniPrimary (citable) accession number: O34816
Secondary accession number(s): Q796K7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: January 1, 1998
Last modified: November 30, 2016
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Regulated by SigK. Could also be negatively regulated by GerE. Transcribed by SigK RNA polymerase.
Inactivation of the ykuD gene does not affect vegetative growth, spore resistance to heat, chloroform and lysozyme, or spore germination in the presence of L-alanine.

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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.