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Protein

Putative L,D-transpeptidase YkuD

Gene

ykuD

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

Functioni

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

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.

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

Keywordsi

Molecular functionGlycosyltransferase, Hydrolase, Transferase
Biological processCell 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
MEROPSiC82.003

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

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

Phylogenomic databases

eggNOGiENOG4107Y2H Bacteria
COG1376 LUCA
HOGENOMiHOG000009616
InParanoidiO34816
OMAiKAVSKGC
PhylomeDBiO34816

Family and domain databases

CDDicd00118 LysM, 1 hit
Gene3Di2.40.440.10, 1 hit
3.10.350.10, 1 hit
InterProiView protein in InterPro
IPR005490 LD_TPept_cat_dom
IPR018392 LysM_dom
IPR036779 LysM_dom_sf
IPR038063 Transpep_catalytic_dom
PfamiView protein in Pfam
PF01476 LysM, 1 hit
PF03734 YkuD, 1 hit
SMARTiView protein in SMART
SM00257 LysM, 1 hit
SUPFAMiSSF141523 SSF141523, 1 hit
PROSITEiView protein in PROSITE
PS51782 LYSM, 1 hit

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, NZ_JNCM01000035.1

Genome annotation databases

EnsemblBacteriaiCAB13277; CAB13277; BSU14040
GeneIDi939216
KEGGibsu:BSU14040
PATRICifig|224308.43.peg.1488

Similar proteinsi

Entry informationi

Entry nameiYKUD_BACSU
AccessioniPrimary (citable) accession number: O34816
Secondary accession number(s): Q796K7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: January 1, 1998
Last modified: March 28, 2018
This is version 109 of the entry and version 1 of the sequence. See 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. 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

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