CAZyme Information: MGYG000000012_00634

Basic Information

• Species: Bacillus subtilis
• Lineage: Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus; Bacillus subtilis
• CAZyme ID: MGYG000000012_00634
• CAZy Family: CBM50
• CAZyme Description: Putative L,D-transpeptidase YkuD

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
167		18117.03	10.7134

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000000012	4053580	Isolate	United Kingdom	Europe

• Gene Location: Start: 584271; End: 584774 Strand: -

Full Sequence      

MRKLLTYQVKQGDTLNSIAADFRISTAALLQVNPSLQAGLTAGQTIVIPGLPDPHTIPYH
IAVSIGAKTLTLFQNNRVIKTYPIAVGKILTQTPTGEFYIINRQRNPGGPFGAYWLSLSK
QHYGIHGTNNPASIGKAVSKGCIRMQNKDVIELASIVPNGTRVLINR

Enzyme Prediction     

No EC number prediction in MGYG000000012_00634.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd16913	YkuD_like	3.14e-39	60	165	1	120	L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD. Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.
COG1376	ErfK	1.89e-27	17	165	73	228	Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis].
pfam03734	YkuD	2.02e-21	58	165	1	89	L,D-transpeptidase catalytic domain. This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.
PRK10260	PRK10260	1.05e-14	9	163	45	231	L,D-transpeptidase; Provisional
PRK10190	PRK10190	3.63e-12	5	165	38	230	L,D-transpeptidase; Provisional

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QRZ94895.1	3.52e-116	4	167	1	164
ASB63406.1	7.11e-116	4	167	1	164
AUS14634.1	7.11e-116	4	167	1	164
AUZ41363.1	2.04e-115	4	167	1	164
APH68305.1	1.31e-114	1	167	1	167

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2MTZ_A	1.74e-113	2	167	2	167	Haddockmodel of Bacillus subtilis L,D-transpeptidase in complex with a peptidoglycan hexamuropeptide [Bacillus subtilis],3ZQD_A B. subtilis L,D-transpeptidase [Bacillus subtilis subsp. subtilis str. 168],4A52_A NMR structure of the imipenem-acylated L,D-transpeptidase from Bacillus subtilis [Bacillus subtilis subsp. subtilis str. 168]
4A1I_A	5.61e-110	4	167	2	165	ykudfrom B.subtilis [Bacillus subtilis],4A1I_B ykud from B.subtilis [Bacillus subtilis],4A1I_C ykud from B.subtilis [Bacillus subtilis],4A1I_D ykud from B.subtilis [Bacillus subtilis],4A1I_E ykud from B.subtilis [Bacillus subtilis],4A1I_F ykud from B.subtilis [Bacillus subtilis],4A1I_G ykud from B.subtilis [Bacillus subtilis],4A1I_H ykud from B.subtilis [Bacillus subtilis],4A1J_A Ykud L,D-transpeptidase from B.subtilis [Bacillus subtilis],4A1J_B Ykud L,D-transpeptidase from B.subtilis [Bacillus subtilis]
1Y7M_A	1.82e-108	5	167	2	164	ChainA, Crystal Structure of the B. subtilis YkuD protein at 2 A resolution [Bacillus subtilis subsp. subtilis str. 168],1Y7M_B Chain B, Crystal Structure of the B. subtilis YkuD protein at 2 A resolution [Bacillus subtilis subsp. subtilis str. 168]
4A1K_A	1.88e-108	4	167	2	165	YkudL,D-transpeptidase [Bacillus subtilis]
6V45_A	6.38e-07	107	165	146	208	Crystalstructure of a Probable carnitine operon oxidoreductase caia from Brucella melitensis [Brucella melitensis bv. 1 str. 16M]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
O34816	4.39e-111	4	167	1	164	Putative L,D-transpeptidase YkuD OS=Bacillus subtilis (strain 168) OX=224308 GN=ykuD PE=1 SV=1
Q65K99	3.70e-85	4	165	1	163	Putative L,D-transpeptidase YkuD OS=Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46) OX=279010 GN=BLi01617 PE=3 SV=1
Q5WC42	3.76e-71	7	165	4	163	Putative L,D-transpeptidase YkuD OS=Alkalihalobacillus clausii (strain KSM-K16) OX=66692 GN=ABC3535 PE=3 SV=1
P54539	8.57e-20	48	165	23	150	Putative L,D-transpeptidase YqjB OS=Bacillus subtilis (strain 168) OX=224308 GN=yqjB PE=3 SV=1
P76193	1.05e-12	6	165	41	232	Probable L,D-transpeptidase YnhG OS=Escherichia coli (strain K12) OX=83333 GN=ynhG PE=1 SV=1

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000012	0.000034	0.000003	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000000012_00634.