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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.4.2.2
- Transferred entry: 4.2.2.20 and 4.2.2.21.
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Reaction:
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Eliminative degradation of polysaccharides containing 1,4-beta-D- hexosaminyl and 1,3-beta-D-glucuronosyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups.
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Gene Ontology (GO) functional annotation
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Biological process
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cell wall macromolecule catabolic process
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1 term
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DOI no:
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J Mol Biol
299:1113-1119
(2000)
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PubMed id:
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The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD).
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A.Bateman,
M.Bycroft.
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ABSTRACT
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The LysM domain is a widespread protein module. It was originally identified in
enzymes that degrade bacterial cell walls but is also present in many other
bacterial proteins. Several proteins that contain the domain, such as
Staphylococcal IgG binding proteins and Escherichia coli intimin, are involved
in bacterial pathogenesis. LysM domains are also found in some eukaryotic
proteins, apparently as a result of horizontal gene transfer from bacteria. The
available evidence suggests that the LysM domain is a general
peptidoglycan-binding module. We have determined the structure of this domain
from E. coli membrane-bound lytic murein transglycosylase D. The LysM domain has
a betaalphaalphabeta secondary structure with the two helices packing onto the
same side of an anti- parallel beta sheet. The structure shows no similarity to
other bacterial cell surface domains. A potential binding site in a shallow
groove on surface of the protein has been identified.
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Selected figure(s)
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Figure 3.
Figure 3. Structure-based alignment of representative
sequences of LysM domains.
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Figure 5.
Figure 5. Structure of the LysM domain showing the position
of Asp11 in the putative ligand binding site.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
299,
1113-1119)
copyright 2000.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.J.Lowe,
C.L.Bardliving,
C.J.Huang,
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K.A.Anderson,
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L.J.Old,
and
C.A.Batt
(2011).
Expression and purification of cGMP grade NY-ESO-1 for clinical trials.
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Biotechnol Prog, 27,
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E.M.Scheurwater,
and
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FEMS Microbiol Lett, 318,
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Theor Appl Genet, 122,
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YneA, an SOS-induced inhibitor of cell division in Bacillus subtilis, is regulated posttranslationally and requires the transmembrane region for activity.
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| |
J Bacteriol, 192,
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Characterization of Acp, a peptidoglycan hydrolase of Clostridium perfringens with N-acetylglucosaminidase activity that is implicated in cell separation and stress-induced autolysis.
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J Bacteriol, 192,
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G.R.Visweswaran,
B.W.Dijkstra,
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Archaea, 2010,
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PLoS One, 5,
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Rapid multiplex detection and differentiation of Listeria cells by use of fluorescent phage endolysin cell wall binding domains.
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Appl Environ Microbiol, 76,
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Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria.
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Proteomics, 9,
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and
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Identification of secreted and surface proteins from Enterococcus faecalis.
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Can J Microbiol, 55,
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A.Tidhar,
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Y.Levi,
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D.Gur,
M.Aftalion,
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A.Zvi,
A.Shafferman,
and
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(2009).
The NlpD lipoprotein is a novel Yersinia pestis virulence factor essential for the development of plague.
|
| |
PLoS One, 4,
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B.Vidová,
M.Chotár,
and
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(2009).
N-terminal anchor in surface immunogenic protein of Streptococcus agalactiae and its influence on immunity elicitation.
|
| |
Folia Microbiol (Praha), 54,
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C.Czaplewski,
S.Kalinowski,
A.Liwo,
and
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(2009).
Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.
|
| |
J Chem Theory Comput, 5,
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G.Zeng,
J.Chen,
L.Zhong,
R.Wang,
L.Jiang,
J.Cai,
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D.Huang,
C.Y.Chen,
and
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(2009).
NSOM- and AFM-based nanotechnology elucidates nano-structural and atomic-force features of a Y. pestis V immunogen-containing particle vaccine capable of eliciting robust response.
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Proteomics, 9,
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K.Kuroda,
and
M.Ueda
(2009).
Cell-surface modification of non-GMO without chemical treatment by novel GMO-coupled and -separated cocultivation method.
|
| |
Appl Microbiol Biotechnol, 82,
293-301.
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Q.Xu,
S.Sudek,
D.McMullan,
M.D.Miller,
B.Geierstanger,
D.H.Jones,
S.S.Krishna,
G.Spraggon,
B.Bursalay,
P.Abdubek,
C.Acosta,
E.Ambing,
T.Astakhova,
H.L.Axelrod,
D.Carlton,
J.Caruthers,
H.J.Chiu,
T.Clayton,
M.C.Deller,
L.Duan,
Y.Elias,
M.A.Elsliger,
J.Feuerhelm,
S.K.Grzechnik,
J.Hale,
G.Won Han,
J.Haugen,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
P.Kozbial,
A.Kumar,
D.Marciano,
A.T.Morse,
E.Nigoghossian,
L.Okach,
S.Oommachen,
J.Paulsen,
R.Reyes,
C.L.Rife,
C.V.Trout,
H.van den Bedem,
D.Weekes,
A.White,
G.Wolf,
C.Zubieta,
K.O.Hodgson,
J.Wooley,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
and
I.A.Wilson
(2009).
Structural basis of murein peptide specificity of a gamma-D-glutamyl-l-diamino acid endopeptidase.
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Structure, 17,
303-313.
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PDB codes:
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R.de Jonge,
and
B.P.Thomma
(2009).
Fungal LysM effectors: extinguishers of host immunity?
|
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Trends Microbiol, 17,
151-157.
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S.K.Gomez,
H.Javot,
P.Deewatthanawong,
I.Torres-Jerez,
Y.Tang,
E.B.Blancaflor,
M.K.Udvardi,
and
M.J.Harrison
(2009).
Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis.
|
| |
BMC Plant Biol, 9,
10.
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|
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T.J.Reilly,
D.L.Chance,
M.J.Calcutt,
J.J.Tanner,
R.L.Felts,
S.C.Waller,
M.T.Henzl,
T.P.Mawhinney,
I.K.Ganjam,
and
W.H.Fales
(2009).
Characterization of a unique class C acid phosphatase from Clostridium perfringens.
|
| |
Appl Environ Microbiol, 75,
3745-3754.
|
|
|
|
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|
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X.C.Zhang,
S.B.Cannon,
and
G.Stacey
(2009).
Evolutionary genomics of LysM genes in land plants.
|
| |
BMC Evol Biol, 9,
183.
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X.Shao,
M.Jiang,
Z.Yu,
H.Cai,
and
L.Li
(2009).
Surface display of heterologous proteins in Bacillus thuringiensis using a peptidoglycan hydrolase anchor.
|
| |
Microb Cell Fact, 8,
48.
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A.A.Nickson,
K.E.Stoll,
and
J.Clarke
(2008).
Folding of a LysM domain: entropy-enthalpy compensation in the transition state of an ideal two-state folder.
|
| |
J Mol Biol, 380,
557-569.
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A.S.Attia,
J.L.Sedillo,
W.Wang,
W.Liu,
C.A.Brautigam,
W.Winkler,
and
E.J.Hansen
(2008).
Moraxella catarrhalis expresses an unusual Hfq protein.
|
| |
Infect Immun, 76,
2520-2530.
|
|
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|
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|
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G.Andre,
K.Leenhouts,
P.Hols,
and
Y.F.Dufrêne
(2008).
Detection and localization of single LysM-peptidoglycan interactions.
|
| |
J Bacteriol, 190,
7079-7086.
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|
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G.Buist,
A.Steen,
J.Kok,
and
O.P.Kuipers
(2008).
LysM, a widely distributed protein motif for binding to (peptido)glycans.
|
| |
Mol Microbiol, 68,
838-847.
|
|
|
|
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H.Yamamoto,
Y.Miyake,
M.Hisaoka,
S.Kurosawa,
and
J.Sekiguchi
(2008).
The major and minor wall teichoic acids prevent the sidewall localization of vegetative DL-endopeptidase LytF in Bacillus subtilis.
|
| |
Mol Microbiol, 70,
297-310.
|
|
|
|
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|
|
M.D.Bolton,
H.P.van Esse,
J.H.Vossen,
R.de Jonge,
I.Stergiopoulos,
I.J.Stulemeijer,
G.C.van den Berg,
O.Borrás-Hidalgo,
H.L.Dekker,
C.G.de Koster,
P.J.de Wit,
M.H.Joosten,
and
B.P.Thomma
(2008).
The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species.
|
| |
Mol Microbiol, 69,
119-136.
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S.Ragumani,
D.Kumaran,
S.K.Burley,
and
S.Swaminathan
(2008).
Crystal structure of a putative lysostaphin peptidase from Vibrio cholerae.
|
| |
Proteins, 72,
1096-1103.
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PDB code:
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S.Tarahomjoo,
Y.Katakura,
and
S.Shioya
(2008).
Expression of C-terminal repeat region of peptidoglycan hydrolase of Lactococcus lactis IL1403 in methylotrophic yeast Pichia pastoris.
|
| |
J Biosci Bioeng, 105,
134-139.
|
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S.Zhao,
and
X.Qi
(2008).
Signaling in plant disease resistance and symbiosis.
|
| |
J Integr Plant Biol, 50,
799-807.
|
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T.M.Mittelmeier,
P.Berthold,
A.Danon,
M.R.Lamb,
A.Levitan,
M.E.Rice,
and
C.L.Dieckmann
(2008).
C2 domain protein MIN1 promotes eyespot organization in Chlamydomonas reinhardtii.
|
| |
Eukaryot Cell, 7,
2100-2112.
|
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T.Ohnuma,
S.Onaga,
K.Murata,
T.Taira,
and
E.Katoh
(2008).
LysM domains from Pteris ryukyuensis chitinase-A: a stability study and characterization of the chitin-binding site.
|
| |
J Biol Chem, 283,
5178-5187.
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W.A.Kaserer,
X.Jiang,
Q.Xiao,
D.C.Scott,
M.Bauler,
D.Copeland,
S.M.Newton,
and
P.E.Klebba
(2008).
Insight from TonB hybrid proteins into the mechanism of iron transport through the outer membrane.
|
| |
J Bacteriol, 190,
4001-4016.
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W.Vollmer,
B.Joris,
P.Charlier,
and
S.Foster
(2008).
Bacterial peptidoglycan (murein) hydrolases.
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| |
FEMS Microbiol Rev, 32,
259-286.
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H.Bierne,
and
P.Cossart
(2007).
Listeria monocytogenes surface proteins: from genome predictions to function.
|
| |
Microbiol Mol Biol Rev, 71,
377-397.
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L.Sasková,
L.Nováková,
M.Basler,
and
P.Branny
(2007).
Eukaryotic-type serine/threonine protein kinase StkP is a global regulator of gene expression in Streptococcus pneumoniae.
|
| |
J Bacteriol, 189,
4168-4179.
|
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|
|
|
|
N.J.Oldfield,
S.J.Bland,
M.Taraktsoglou,
F.J.Dos Ramos,
K.Robinson,
K.G.Wooldridge,
and
D.A.Ala'Aldeen
(2007).
T-cell stimulating protein A (TspA) of Neisseria meningitidis is required for optimal adhesion to human cells.
|
| |
Cell Microbiol, 9,
463-478.
|
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|
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|
P.C.Soo,
Y.T.Horng,
M.J.Lai,
J.R.Wei,
S.C.Hsieh,
Y.L.Chang,
Y.H.Tsai,
and
H.C.Lai
(2007).
Pirin regulates pyruvate catabolism by interacting with the pyruvate dehydrogenase E1 subunit and modulating pyruvate dehydrogenase activity.
|
| |
J Bacteriol, 189,
109-118.
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Q.H.Shen,
and
P.Schulze-Lefert
(2007).
Rumble in the nuclear jungle: compartmentalization, trafficking, and nuclear action of plant immune receptors.
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| |
EMBO J, 26,
4293-4301.
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S.Radutoiu,
L.H.Madsen,
E.B.Madsen,
A.Jurkiewicz,
E.Fukai,
E.M.Quistgaard,
A.S.Albrektsen,
E.K.James,
S.Thirup,
and
J.Stougaard
(2007).
LysM domains mediate lipochitin-oligosaccharide recognition and Nfr genes extend the symbiotic host range.
|
| |
EMBO J, 26,
3923-3935.
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Y.Redko,
P.Courtin,
C.Mézange,
C.Huard,
and
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(2007).
Lactococcus lactis gene yjgB encodes a gamma-D-glutaminyl-L-lysyl-endopeptidase which hydrolyzes peptidoglycan.
|
| |
Appl Environ Microbiol, 73,
5825-5831.
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A.Chauhan,
H.Lofton,
E.Maloney,
J.Moore,
M.Fol,
M.V.Madiraju,
and
M.Rajagopalan
(2006).
Interference of Mycobacterium tuberculosis cell division by Rv2719c, a cell wall hydrolase.
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Mol Microbiol, 62,
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A.J.Nowalk,
R.D.Gilmore,
and
J.A.Carroll
(2006).
Serologic proteome analysis of Borrelia burgdorferi membrane-associated proteins.
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| |
Infect Immun, 74,
3864-3873.
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A.Lee,
and
A.M.Hirsch
(2006).
Signals and Responses: Choreographing the Complex Interaction between Legumes and alpha- and beta-Rhizobia.
|
| |
Plant Signal Behav, 1,
161-168.
|
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A.Melillo,
D.D.Sledjeski,
S.Lipski,
R.M.Wooten,
V.Basrur,
and
E.R.Lafontaine
(2006).
Identification of a Francisella tularensis LVS outer membrane protein that confers adherence to A549 human lung cells.
|
| |
FEMS Microbiol Lett, 263,
102-108.
|
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C.Eckert,
M.Lecerf,
L.Dubost,
M.Arthur,
and
S.Mesnage
(2006).
Functional analysis of AtlA, the major N-acetylglucosaminidase of Enterococcus faecalis.
|
| |
J Bacteriol, 188,
8513-8519.
|
|
|
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|
|
E.Griffiths,
M.S.Ventresca,
and
R.S.Gupta
(2006).
BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species.
|
| |
BMC Genomics, 7,
14.
|
|
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|
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G.V.Mukamolova,
A.G.Murzin,
E.G.Salina,
G.R.Demina,
D.B.Kell,
A.S.Kaprelyants,
and
M.Young
(2006).
Muralytic activity of Micrococcus luteus Rpf and its relationship to physiological activity in promoting bacterial growth and resuscitation.
|
| |
Mol Microbiol, 59,
84-98.
|
|
|
|
|
|
|
H.Zhu,
B.K.Riely,
N.J.Burns,
and
J.M.Ané
(2006).
Tracing nonlegume orthologs of legume genes required for nodulation and arbuscular mycorrhizal symbioses.
|
| |
Genetics, 172,
2491-2499.
|
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|
|
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|
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J.Bielnicki,
Y.Devedjiev,
U.Derewenda,
Z.Dauter,
A.Joachimiak,
and
Z.S.Derewenda
(2006).
B. subtilis ykuD protein at 2.0 A resolution: insights into the structure and function of a novel, ubiquitous family of bacterial enzymes.
|
| |
Proteins, 62,
144-151.
|
|
|
PDB code:
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|
|
J.R.Scott,
and
T.C.Barnett
(2006).
Surface proteins of gram-positive bacteria and how they get there.
|
| |
Annu Rev Microbiol, 60,
397-423.
|
|
|
|
|
|
|
M.Nanias,
C.Czaplewski,
and
H.A.Scheraga
(2006).
Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field.
|
| |
J Chem Theory Comput, 2,
513-528.
|
|
|
|
|
|
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M.R.Pourmand,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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