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N-acetylmuramoyl-L-alanine amidase Rv3717 (EC 3.5.1.28) (Zinc-dependent peptidoglycan amidase)

 PEPAM_MYCTU             Reviewed;         241 AA.
I6Y4D2;
09-DEC-2015, integrated into UniProtKB/Swiss-Prot.
03-OCT-2012, sequence version 1.
12-SEP-2018, entry version 43.
RecName: Full=N-acetylmuramoyl-L-alanine amidase Rv3717 {ECO:0000303|PubMed:24019530, ECO:0000303|PubMed:24311595};
EC=3.5.1.28 {ECO:0000269|PubMed:24019530, ECO:0000269|PubMed:24311595};
AltName: Full=Zinc-dependent peptidoglycan amidase {ECO:0000303|PubMed:24019530};
Flags: Precursor;
OrderedLocusNames=Rv3717 {ECO:0000312|EMBL:CCP46543.1};
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[3]
X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) OF 25-241 IN COMPLEX WITH ZINC,
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR,
ACTIVITY REGULATION, SUBUNIT, AND PATHWAY.
STRAIN=H37Rv;
PubMed=24311595; DOI=10.1107/S0907444913026371;
Kumar A., Kumar S., Kumar D., Mishra A., Dewangan R.P.,
Shrivastava P., Ramachandran S., Taneja B.;
"The structure of Rv3717 reveals a novel amidase from Mycobacterium
tuberculosis.";
Acta Crystallogr. D 69:2543-2554(2013).
[4]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 20-241 OF APOENZYME AND IN
COMPLEXES WITH ZINC AND THE DIPEPTIDE PRODUCT
L-ALANINE-ISO-D-GLUTAMINE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
DISULFIDE BOND, MUTAGENESIS OF GLU-200, ACTIVE SITE, AND PATHWAY.
PubMed=24019530; DOI=10.1074/jbc.M113.510792;
Prigozhin D.M., Mavrici D., Huizar J.P., Vansell H.J., Alber T.;
"Structural and biochemical analyses of Mycobacterium tuberculosis N-
acetylmuramyl-L-alanine amidase Rv3717 point to a role in
peptidoglycan fragment recycling.";
J. Biol. Chem. 288:31549-31555(2013).
-!- FUNCTION: Cell-wall hydrolase that hydrolyzes the amide bond
between N-acetylmuramic acid and L-alanine in cell-wall
glycopeptides (PubMed:24311595, PubMed:24019530). Is able to
hydrolyze the cell walls of several bacterial species (i.e.
Paenibacillus sp., B.avium, E.coli DH5alpha, E.aerogenes,
L.acidophilus, B.thuringiensis, B.pumilus, B.subtilis and E.coli
W3110), thereby showing that it is a cell-wall hydrolase with
broad-spectrum activity (PubMed:24311595). May have a role in
peptidoglycan fragment recycling (PubMed:24019530).
{ECO:0000269|PubMed:24019530, ECO:0000269|PubMed:24311595}.
-!- CATALYTIC ACTIVITY: Hydrolyzes the link between N-acetylmuramoyl
residues and L-amino acid residues in certain cell-wall
glycopeptides. {ECO:0000269|PubMed:24019530,
ECO:0000269|PubMed:24311595}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:24019530,
ECO:0000269|PubMed:24311595};
-!- ACTIVITY REGULATION: The structure reveals a short flexible
hairpin turn that partially occludes the active site and may be
involved in autoregulation. {ECO:0000305|PubMed:24311595}.
-!- PATHWAY: Cell wall degradation; peptidoglycan degradation.
{ECO:0000269|PubMed:24019530, ECO:0000269|PubMed:24311595}.
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:24311595}.
-!- SUBCELLULAR LOCATION: Periplasm {ECO:0000305|PubMed:24019530}.
-!- MISCELLANEOUS: Disulfide oxidation is not required for folding of
the enzyme core or in vitro muramyl dipeptide hydrolysis.
{ECO:0000269|PubMed:24019530}.
-!- SIMILARITY: Belongs to the N-acetylmuramoyl-L-alanine amidase 3
family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL123456; CCP46543.1; -; Genomic_DNA.
RefSeq; NP_218234.1; NC_000962.3.
RefSeq; WP_003420410.1; NZ_KK339374.1.
PDB; 4LQ6; X-ray; 1.68 A; A=25-241.
PDB; 4M6G; X-ray; 2.10 A; A=20-241.
PDB; 4M6H; X-ray; 2.19 A; A/B=20-241.
PDB; 4M6I; X-ray; 2.67 A; A/B=20-241.
PDBsum; 4LQ6; -.
PDBsum; 4M6G; -.
PDBsum; 4M6H; -.
PDBsum; 4M6I; -.
ProteinModelPortal; I6Y4D2; -.
SMR; I6Y4D2; -.
STRING; 83332.Rv3717; -.
PaxDb; I6Y4D2; -.
PRIDE; I6Y4D2; -.
EnsemblBacteria; CCP46543; CCP46543; Rv3717.
GeneID; 885602; -.
KEGG; mtu:Rv3717; -.
KEGG; mtv:RVBD_3717; -.
PATRIC; fig|83332.111.peg.4133; -.
TubercuList; Rv3717; -.
eggNOG; ENOG4108RU2; Bacteria.
eggNOG; COG0860; LUCA.
KO; K01448; -.
OMA; KECDTTG; -.
PhylomeDB; I6Y4D2; -.
UniPathway; UPA00549; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0030288; C:outer membrane-bounded periplasmic space; IBA:GO_Central.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008745; F:N-acetylmuramoyl-L-alanine amidase activity; IBA:GO_Central.
GO; GO:0016998; P:cell wall macromolecule catabolic process; IEA:UniProtKB-UniPathway.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0009253; P:peptidoglycan catabolic process; IEA:InterPro.
CDD; cd02696; MurNAc-LAA; 1.
InterPro; IPR002508; MurNAc-LAA_cat.
Pfam; PF01520; Amidase_3; 1.
SMART; SM00646; Ami_3; 1.
1: Evidence at protein level;
3D-structure; Cell wall biogenesis/degradation; Complete proteome;
Disulfide bond; Hydrolase; Metal-binding; Periplasm;
Reference proteome; Signal; Zinc.
SIGNAL 1 24 {ECO:0000255}.
CHAIN 25 241 N-acetylmuramoyl-L-alanine amidase
Rv3717.
/FTId=PRO_5004159884.
DOMAIN 29 230 MurNAc-LAA. {ECO:0000255}.
ACT_SITE 200 200 Proton donor/acceptor.
{ECO:0000305|PubMed:24019530}.
METAL 35 35 Zinc; via tele nitrogen.
{ECO:0000244|PDB:4LQ6,
ECO:0000244|PDB:4M6G,
ECO:0000244|PDB:4M6I,
ECO:0000269|PubMed:24019530,
ECO:0000269|PubMed:24311595}.
METAL 70 70 Zinc. {ECO:0000244|PDB:4LQ6,
ECO:0000244|PDB:4M6G,
ECO:0000244|PDB:4M6I,
ECO:0000269|PubMed:24019530,
ECO:0000269|PubMed:24311595}.
METAL 125 125 Zinc; via pros nitrogen.
{ECO:0000244|PDB:4LQ6,
ECO:0000244|PDB:4M6G,
ECO:0000244|PDB:4M6I,
ECO:0000269|PubMed:24019530,
ECO:0000269|PubMed:24311595}.
DISULFID 57 105 {ECO:0000269|PubMed:24019530}.
MUTAGEN 200 200 E->A,Q: Loss of catalytic activity.
{ECO:0000269|PubMed:24019530}.
SEQUENCE 241 AA; 24836 MW; 719D0F523A4B9C0C CRC64;
MIVGVLVAAA TPIISSASAT PANIAGMVVF IDPGHNGAND ASIGRQVPTG RGGTKNCQAS
GTSTNSGYPE HTFTWETGLR LRAALNALGV RTALSRGNDN ALGPCVDERA NMANALRPNA
IVSLHADGGP ASGRGFHVNY SAPPLNAIQA GPSVQFARIM RDQLQASGIP KANYIGQDGL
YGRSDLAGLN LAQYPSILVE LGNMKNPADS ALMESAEGRQ KYANALVRGV AGFLATQGQA
R


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