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Protein

LysM and putative peptidoglycan-binding domain-containing protein 1

Gene

LYSMD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Experimental evidence at protein leveli

Names & Taxonomyi

Protein namesi
Recommended name:
LysM and putative peptidoglycan-binding domain-containing protein 1
Gene namesi
Name:LYSMD1
ORF Names:SB145
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:32070. LYSMD1.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA142671493.

Polymorphism and mutation databases

BioMutaiLYSMD1.
DMDMi74752122.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 227227LysM and putative peptidoglycan-binding domain-containing protein 1PRO_0000247996Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei23 – 231PhosphoserineCombined sources
Modified residuei33 – 331PhosphoserineCombined sources
Modified residuei99 – 991PhosphoserineCombined sources
Modified residuei166 – 1661PhosphoserineCombined sources
Modified residuei194 – 1941PhosphoserineBy similarity
Modified residuei212 – 2121PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ96S90.
MaxQBiQ96S90.
PaxDbiQ96S90.
PeptideAtlasiQ96S90.
PRIDEiQ96S90.

PTM databases

iPTMnetiQ96S90.
PhosphoSiteiQ96S90.

Expressioni

Gene expression databases

BgeeiQ96S90.
CleanExiHS_LYSMD1.
GenevisibleiQ96S90. HS.

Organism-specific databases

HPAiHPA028055.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
GOLGA2Q083793EBI-10293291,EBI-618309
MTUS2Q5JR593EBI-10293291,EBI-742948
TCF12Q990813EBI-10293291,EBI-722877

Protein-protein interaction databases

BioGridi132813. 4 interactions.
IntActiQ96S90. 3 interactions.
STRINGi9606.ENSP00000357904.

Structurei

Secondary structure

1
227
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi37 – 426Combined sources
Helixi50 – 578Combined sources
Helixi61 – 677Combined sources
Helixi76 – 783Combined sources
Beta strandi82 – 876Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DJPNMR-A32-95[»]
ProteinModelPortaliQ96S90.
SMRiQ96S90. Positions 34-95.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ96S90.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini40 – 8445LysMPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 LysM domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410J1FK. Eukaryota.
ENOG4111TII. LUCA.
GeneTreeiENSGT00520000055632.
HOGENOMiHOG000290644.
HOVERGENiHBG079723.
InParanoidiQ96S90.
OMAiHLSSPRM.
OrthoDBiEOG7H1JPH.
PhylomeDBiQ96S90.
TreeFamiTF318444.

Family and domain databases

Gene3Di3.10.350.10. 1 hit.
InterProiIPR018392. LysM_dom.
[Graphical view]
PfamiPF01476. LysM. 1 hit.
[Graphical view]
SMARTiSM00257. LysM. 1 hit.
[Graphical view]
SUPFAMiSSF54106. SSF54106. 1 hit.
PROSITEiPS51782. LYSM. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q96S90-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MASPSRQPPP GGSGLLQGSR ARSYGSLVQS ACSPVRERRL EHQLEPGDTL
60 70 80 90 100
AGLALKYGVT MEQIKRANRL YTNDSIFLKK TLYIPILTEP RDLFNGLDSE
110 120 130 140 150
EEKDGEEKVH PSNSEVWPHS TERKKQETGA GRANGEVLPT PGQETPTPIH
160 170 180 190 200
DLSASDFLKK LDSQISLSKK AAAQKLKKGE NGVPGEDAGL HLSSPWMQQR
210 220
AVLGPVPLTR TSRTRTLRDQ EDEIFKL
Length:227
Mass (Da):25,003
Last modified:December 1, 2001 - v1
Checksum:i3F119652D42F224F
GO
Isoform 2 (identifier: Q96S90-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-60: MASPSRQPPPGGSGLLQGSRARSYGSLVQSACSPVRERRLEHQLEPGDTLAGLALKYGVT → MRSGPLRISEWK

Show »
Length:179
Mass (Da):20,171
Checksum:i3490AA3ACB0F1AE9
GO

Sequence cautioni

The sequence CAH10716.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti128 – 1281T → G in CAH10716 (PubMed:17974005).Curated
Sequence conflicti164 – 1641Q → R in BAG60863 (PubMed:14702039).Curated
Sequence conflicti198 – 1981Q → R in CAH10716 (PubMed:17974005).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 6060MASPS…KYGVT → MRSGPLRISEWK in isoform 2. 1 PublicationVSP_041083Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY037156 mRNA. Translation: AAK67635.1.
AK298706 mRNA. Translation: BAG60863.1.
AL122088 mRNA. Translation: CAH10716.1. Different initiation.
BX647911 mRNA. Translation: CAH10574.1.
AL592424 Genomic DNA. Translation: CAI16380.1.
BC031649 mRNA. Translation: AAH31649.1.
CCDSiCCDS44218.1. [Q96S90-2]
CCDS986.1. [Q96S90-1]
RefSeqiNP_001130015.1. NM_001136543.1. [Q96S90-2]
NP_997716.1. NM_212551.4. [Q96S90-1]
UniGeneiHs.591482.

Genome annotation databases

EnsembliENST00000368908; ENSP00000357904; ENSG00000163155. [Q96S90-1]
ENST00000440902; ENSP00000404059; ENSG00000163155. [Q96S90-2]
GeneIDi388695.
KEGGihsa:388695.
UCSCiuc001ewy.4. human. [Q96S90-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY037156 mRNA. Translation: AAK67635.1.
AK298706 mRNA. Translation: BAG60863.1.
AL122088 mRNA. Translation: CAH10716.1. Different initiation.
BX647911 mRNA. Translation: CAH10574.1.
AL592424 Genomic DNA. Translation: CAI16380.1.
BC031649 mRNA. Translation: AAH31649.1.
CCDSiCCDS44218.1. [Q96S90-2]
CCDS986.1. [Q96S90-1]
RefSeqiNP_001130015.1. NM_001136543.1. [Q96S90-2]
NP_997716.1. NM_212551.4. [Q96S90-1]
UniGeneiHs.591482.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DJPNMR-A32-95[»]
ProteinModelPortaliQ96S90.
SMRiQ96S90. Positions 34-95.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi132813. 4 interactions.
IntActiQ96S90. 3 interactions.
STRINGi9606.ENSP00000357904.

PTM databases

iPTMnetiQ96S90.
PhosphoSiteiQ96S90.

Polymorphism and mutation databases

BioMutaiLYSMD1.
DMDMi74752122.

Proteomic databases

EPDiQ96S90.
MaxQBiQ96S90.
PaxDbiQ96S90.
PeptideAtlasiQ96S90.
PRIDEiQ96S90.

Protocols and materials databases

DNASUi388695.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000368908; ENSP00000357904; ENSG00000163155. [Q96S90-1]
ENST00000440902; ENSP00000404059; ENSG00000163155. [Q96S90-2]
GeneIDi388695.
KEGGihsa:388695.
UCSCiuc001ewy.4. human. [Q96S90-1]

Organism-specific databases

CTDi388695.
GeneCardsiLYSMD1.
HGNCiHGNC:32070. LYSMD1.
HPAiHPA028055.
neXtProtiNX_Q96S90.
PharmGKBiPA142671493.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410J1FK. Eukaryota.
ENOG4111TII. LUCA.
GeneTreeiENSGT00520000055632.
HOGENOMiHOG000290644.
HOVERGENiHBG079723.
InParanoidiQ96S90.
OMAiHLSSPRM.
OrthoDBiEOG7H1JPH.
PhylomeDBiQ96S90.
TreeFamiTF318444.

Miscellaneous databases

EvolutionaryTraceiQ96S90.
GenomeRNAii388695.
PROiQ96S90.

Gene expression databases

BgeeiQ96S90.
CleanExiHS_LYSMD1.
GenevisibleiQ96S90. HS.

Family and domain databases

Gene3Di3.10.350.10. 1 hit.
InterProiIPR018392. LysM_dom.
[Graphical view]
PfamiPF01476. LysM. 1 hit.
[Graphical view]
SMARTiSM00257. LysM. 1 hit.
[Graphical view]
SUPFAMiSSF54106. SSF54106. 1 hit.
PROSITEiPS51782. LYSM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Li N., Zhang W., Wan T., Zhang M., Cao X.
    Submitted (MAY-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain and Cervix.
  4. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  6. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-99, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-99, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Toward a comprehensive characterization of a human cancer cell phosphoproteome."
    Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J., Mohammed S.
    J. Proteome Res. 12:260-271(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23; SER-33; SER-99; SER-166 AND SER-212, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma and Erythroleukemia.
  10. "The solution structure of the LYSM domain of human hypothetical protein SB145."
    RIKEN structural genomics initiative (RSGI)
    Submitted (OCT-2006) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 25-95.

Entry informationi

Entry nameiLYSM1_HUMAN
AccessioniPrimary (citable) accession number: Q96S90
Secondary accession number(s): B4DQA1, Q69YX9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 5, 2006
Last sequence update: December 1, 2001
Last modified: July 6, 2016
This is version 116 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.