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Q9Y239 (NOD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 140. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nucleotide-binding oligomerization domain-containing protein 1
Alternative name(s):
Caspase recruitment domain-containing protein 4
Gene names
Name:NOD1
Synonyms:CARD4
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length953 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Enhances caspase-9-mediated apoptosis. Induces NF-kappa-B activity via RIPK2 and IKK-gamma. Confers responsiveness to intracellular bacterial lipopolysaccharides (LPS). Forms an intracellular sensing system along with ARHGEF2 for the detection of microbial effectors during cell invasion by pathogens. Required for RHOA and RIPK2 dependent NF-kappa-B signaling pathway activation upon S.flexneri cell invasion. Involved not only in sensing peptidoglycan (PGN)-derived muropeptides but also in the activation of NF-kappa-B by Shigella effector proteins IpgB2 and OspB. Recruits NLRP10 to the cell membrane following bacterial infection. Ref.5 Ref.7 Ref.8 Ref.11

Subunit structure

Homodimer. Self-associates. Binds to caspase-9 and RIPK2 by CARD-CARD interaction. Interacts with ARHGEF2. Interacts with NLRP10 and recruits it to the cell membrane following invasive bacterial infection. Ref.7 Ref.8 Ref.10 Ref.11 Ref.12

Subcellular location

Cytoplasm. Cell membrane. Apical cell membrane. Basolateral cell membrane. Note: Detected in the cytoplasm and at the cell membrane. Following bacterial infection, localizes to bacterial entry sites in the cell membrane. Recruited to the basolateral and apical membranes in polarized epithelial cells. Ref.6 Ref.7

Tissue specificity

Highly expressed in adult heart, skeletal muscle, pancreas, spleen and ovary. Also detected in placenta, lung, liver, kidney, thymus, testis, small intestine and colon.

Sequence similarities

Contains 1 CARD domain.

Contains 9 LRR (leucine-rich) repeats.

Contains 1 NACHT domain.

Ontologies

Keywords
   Biological processApoptosis
Immunity
Innate immunity
   Cellular componentCell membrane
Cytoplasm
Membrane
   Coding sequence diversityPolymorphism
   DomainLeucine-rich repeat
Repeat
   LigandATP-binding
Nucleotide-binding
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processJNK cascade

Traceable author statement. Source: Reactome

MyD88-dependent toll-like receptor signaling pathway

Traceable author statement. Source: Reactome

MyD88-independent toll-like receptor signaling pathway

Traceable author statement. Source: Reactome

TRIF-dependent toll-like receptor signaling pathway

Traceable author statement. Source: Reactome

activation of MAPK activity

Traceable author statement. Source: Reactome

activation of cysteine-type endopeptidase activity involved in apoptotic process

Inferred from direct assay Ref.2. Source: MGI

apoptotic process

Traceable author statement Ref.2. Source: ProtInc

defense response

Traceable author statement PubMed 15967716. Source: HGNC

defense response to Gram-positive bacterium

Inferred from electronic annotation. Source: Ensembl

defense response to bacterium

Inferred from direct assay PubMed 15653568. Source: HGNC

detection of bacterium

Inferred from direct assay PubMed 15653568. Source: HGNC

detection of biotic stimulus

Traceable author statement PubMed 15967716. Source: HGNC

inflammatory response

Traceable author statement PubMed 15967716. Source: HGNC

innate immune response

Traceable author statement. Source: Reactome

interleukin-8 biosynthetic process

Inferred from direct assay PubMed 15653568. Source: HGNC

intracellular signal transduction

Inferred from direct assay PubMed 15653568. Source: HGNC

nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway

Traceable author statement. Source: Reactome

nucleotide-binding oligomerization domain containing signaling pathway

Traceable author statement. Source: Reactome

positive regulation of ERK1 and ERK2 cascade

Inferred from electronic annotation. Source: Ensembl

positive regulation of I-kappaB kinase/NF-kappaB signaling

Inferred from direct assay Ref.2. Source: MGI

positive regulation of JNK cascade

Inferred from electronic annotation. Source: Ensembl

positive regulation of NF-kappaB transcription factor activity

Inferred from direct assay Ref.11Ref.7. Source: UniProtKB

positive regulation of cysteine-type endopeptidase activity involved in apoptotic process

Inferred from direct assay Ref.2. Source: MGI

positive regulation of dendritic cell antigen processing and presentation

Inferred from sequence or structural similarity. Source: BHF-UCL

positive regulation of interleukin-6 production

Inferred from electronic annotation. Source: Ensembl

positive regulation of tumor necrosis factor production

Inferred from electronic annotation. Source: Ensembl

protein oligomerization

Traceable author statement PubMed 15967716. Source: HGNC

signal transduction

Traceable author statement PubMed 15967716. Source: HGNC

stress-activated MAPK cascade

Traceable author statement. Source: Reactome

toll-like receptor 10 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor 2 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor 3 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor 4 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor 5 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor 9 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor TLR1:TLR2 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor TLR6:TLR2 signaling pathway

Traceable author statement. Source: Reactome

toll-like receptor signaling pathway

Traceable author statement. Source: Reactome

   Cellular_componentapical plasma membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

basolateral plasma membrane

Inferred from direct assay Ref.7. Source: UniProtKB

cytoplasm

Traceable author statement PubMed 15967716. Source: HGNC

cytosol

Traceable author statement. Source: Reactome

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

CARD domain binding

Inferred from direct assay Ref.2. Source: MGI

cysteine-type endopeptidase activator activity involved in apoptotic process

Traceable author statement Ref.2. Source: ProtInc

identical protein binding

Inferred from physical interaction Ref.12. Source: IntAct

peptidoglycan binding

Traceable author statement PubMed 15967716. Source: HGNC

protein homodimerization activity

Inferred from physical interaction Ref.12. Source: UniProtKB

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

itself2EBI-1051262,EBI-1051262

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 953953Nucleotide-binding oligomerization domain-containing protein 1
PRO_0000144077

Regions

Domain15 – 10591CARD
Domain196 – 531336NACHT
Repeat632 – 65625LRR 1
Repeat702 – 72524LRR 2
Repeat727 – 75024LRR 3
Repeat755 – 77824LRR 4
Repeat783 – 80624LRR 5
Repeat839 – 86224LRR 6
Repeat867 – 89125LRR 7
Repeat895 – 91824LRR 8
Repeat923 – 94624LRR 9
Nucleotide binding202 – 2098ATP Potential

Natural variations

Natural variant2661E → K.
Corresponds to variant rs2075820 [ dbSNP | Ensembl ].
VAR_020371
Natural variant3721D → N.
Corresponds to variant rs5743342 [ dbSNP | Ensembl ].
VAR_053624
Natural variant4471R → H. Ref.4
Corresponds to variant rs2975634 [ dbSNP | Ensembl ].
VAR_053625
Natural variant6051R → W.
Corresponds to variant rs5743345 [ dbSNP | Ensembl ].
VAR_053626
Natural variant6101A → T.
Corresponds to variant rs5743346 [ dbSNP | Ensembl ].
VAR_053627

Experimental info

Mutagenesis411V → A: Abolishes interaction with RIPK2/RICK. Ref.2 Ref.11
Mutagenesis411V → Q: Abolishes caspase-9 activation. Ref.2 Ref.11
Mutagenesis441L → A: Abolishes activation of NF-kappa-B. No effect on interaction with RIPK2. Ref.11
Mutagenesis481D → K: Abolishes activation of NF-kappa-B. No effect on interaction with RIPK2. Ref.11
Mutagenesis531E → K: No effect on activation of NF-kappa-B. Abolishes interaction with RIPK2. Ref.11
Mutagenesis541D → K: Abolishes activation of NF-kappa-B. Abolishes interaction with RIPK2. Ref.11
Mutagenesis561E → K: Abolishes activation of NF-kappa-B. Abolishes interaction with RIPK2. Ref.11
Mutagenesis691R → E: Abolishes activation of NF-kappa-B. Abolishes interaction with RIPK2. Ref.11
Mutagenesis2081K → R: Reduces caspase-9 activation. Reduced binding affinity for NLRP10. Does not associate with cell membrane. Ref.2 Ref.6 Ref.8
Mutagenesis2871D → A: Reduced binding affinity for NLRP10. Ref.8
Mutagenesis7111D → S: Does not associate with cell membrane. Ref.6
Mutagenesis7881H → S: No effect on association with cell membrane. Ref.6
Mutagenesis7921G → S: Does not associate with cell membrane. Ref.6
Mutagenesis8771Q → S: Does not associate with cell membrane. Ref.6

Secondary structure

................. 953
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9Y239 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: 0A9DF5FC6487E21A

FASTA953107,691
        10         20         30         40         50         60 
MEEQGHSEME IIPSESHPHI QLLKSNRELL VTHIRNTQCL VDNLLKNDYF SAEDAEIVCA 

        70         80         90        100        110        120 
CPTQPDKVRK ILDLVQSKGE EVSEFFLYLL QQLADAYVDL RPWLLEIGFS PSLLTQSKVV 

       130        140        150        160        170        180 
VNTDPVSRYT QQLRHHLGRD SKFVLCYAQK EELLLEEIYM DTIMELVGFS NESLGSLNSL 

       190        200        210        220        230        240 
ACLLDHTTGI LNEQGETIFI LGDAGVGKSM LLQRLQSLWA TGRLDAGVKF FFHFRCRMFS 

       250        260        270        280        290        300 
CFKESDRLCL QDLLFKHYCY PERDPEEVFA FLLRFPHVAL FTFDGLDELH SDLDLSRVPD 

       310        320        330        340        350        360 
SSCPWEPAHP LVLLANLLSG KLLKGASKLL TARTGIEVPR QFLRKKVLLR GFSPSHLRAY 

       370        380        390        400        410        420 
ARRMFPERAL QDRLLSQLEA NPNLCSLCSV PLFCWIIFRC FQHFRAAFEG SPQLPDCTMT 

       430        440        450        460        470        480 
LTDVFLLVTE VHLNRMQPSS LVQRNTRSPV ETLHAGRDTL CSLGQVAHRG MEKSLFVFTQ 

       490        500        510        520        530        540 
EEVQASGLQE RDMQLGFLRA LPELGPGGDQ QSYEFFHLTL QAFFTAFFLV LDDRVGTQEL 

       550        560        570        580        590        600 
LRFFQEWMPP AGAATTSCYP PFLPFQCLQG SGPAREDLFK NKDHFQFTNL FLCGLLSKAK 

       610        620        630        640        650        660 
QKLLRHLVPA AALRRKRKAL WAHLFSSLRG YLKSLPRVQV ESFNQVQAMP TFIWMLRCIY 

       670        680        690        700        710        720 
ETQSQKVGQL AARGICANYL KLTYCNACSA DCSALSFVLH HFPKRLALDL DNNNLNDYGV 

       730        740        750        760        770        780 
RELQPCFSRL TVLRLSVNQI TDGGVKVLSE ELTKYKIVTY LGLYNNQITD VGARYVTKIL 

       790        800        810        820        830        840 
DECKGLTHLK LGKNKITSEG GKYLALAVKN SKSISEVGMW GNQVGDEGAK AFAEALRNHP 

       850        860        870        880        890        900 
SLTTLSLASN GISTEGGKSL ARALQQNTSL EILWLTQNEL NDEVAESLAE MLKVNQTLKH 

       910        920        930        940        950 
LWLIQNQITA KGTAQLADAL QSNTGITEIC LNGNLIKPEE AKVYEDEKRI ICF 

« Hide

References

« Hide 'large scale' references
[1]"Human CARD4 protein is a novel CED-4/Apaf-1 cell death family member that activates NF-kappaB."
Bertin J., Nir W.-J., Fischer C.M., Tayber O.V., Errada P.R., Grant J.R., Keilty J.J., Gosselin M.L., Robison K.E., Wong G.H.W., Glucksmann M.A., DiStefano P.S.
J. Biol. Chem. 274:12955-12958(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Endothelial cell.
[2]"Nod1, an Apaf-1-like activator of caspase-9 and nuclear factor-kappaB."
Inohara N., Koseki T., del Peso L., Hu Y., Yee C., Chen S., Carrio R., Merino J., Liu D., Ni J., Nunez G.
J. Biol. Chem. 274:14560-14567(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], MUTAGENESIS OF VAL-41 AND LYS-208.
Tissue: Mammary gland.
[3]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"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], VARIANT HIS-447.
Tissue: Lymph.
[5]"Human Nod1 confers responsiveness to bacterial lipopolysaccharides."
Inohara N., Ogura Y., Chen F.F., Muto A., Nunez G.
J. Biol. Chem. 276:2551-2554(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[6]"The pattern-recognition molecule Nod1 is localized at the plasma membrane at sites of bacterial interaction."
Kufer T.A., Kremmer E., Adam A.C., Philpott D.J., Sansonetti P.J.
Cell. Microbiol. 10:477-486(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-208; ASP-711; HIS-788; GLY-792 AND GLN-877.
[7]"GEF-H1 mediated control of NOD1 dependent NF-kappaB activation by Shigella effectors."
Fukazawa A., Alonso C., Kurachi K., Gupta S., Lesser C.F., McCormick B.A., Reinecker H.C.
PLoS Pathog. 4:E1000228-E1000228(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH ARHGEF2.
[8]"NLRP10 enhances Shigella-induced pro-inflammatory responses."
Lautz K., Damm A., Menning M., Wenger J., Adam A.C., Zigrino P., Kremmer E., Kufer T.A.
Cell. Microbiol. 14:1568-1583(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH NLRP10, MUTAGENESIS OF LYS-208 AND ASP-287.
[9]"Solution structure of the CARD domain in human caspase recruitment domain protein 4 (NOD1 protein)."
RIKEN structural genomics initiative (RSGI)
Submitted (DEC-2006) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 14-110.
[10]"Crystal structure of the Nod1 caspase activation and recruitment domain."
Coussens N.P., Mowers J.C., McDonald C., Nunez G., Ramaswamy S.
Biochem. Biophys. Res. Commun. 353:1-5(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 16-108, SUBUNIT.
[11]"Solution structure of NOD1 CARD and mutational analysis of its interaction with the CARD of downstream kinase RICK."
Manon F., Favier A., Nunez G., Simorre J.P., Cusack S.
J. Mol. Biol. 365:160-174(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 15-138, FUNCTION, INTERACTION WITH RIPK2, MUTAGENESIS OF VAL-41; LEU-44; ASP-48; GLU-53; ASP-54; GLU-56 AND ARG-69.
[12]"Monomer/dimer transition of the caspase-recruitment domain of human Nod1."
Srimathi T., Robbins S.L., Dubas R.L., Hasegawa M., Inohara N., Park Y.C.
Biochemistry 47:1319-1325(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 9-106, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF126484 mRNA. Translation: AAD29125.1.
AF149774 Genomic DNA. Translation: AAD43922.1.
AF113925 mRNA. Translation: AAD28350.1.
AC006027 Genomic DNA. Translation: AAS46897.1.
BC040339 mRNA. Translation: AAH40339.1.
RefSeqNP_006083.1. NM_006092.2.
XP_005249625.1. XM_005249568.1.
XP_005249629.1. XM_005249572.1.
UniGeneHs.405153.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2B1WNMR-A15-138[»]
2DBDNMR-A17-110[»]
2NSNX-ray2.00A16-108[»]
2NZ7X-ray1.90A/B9-106[»]
4E9MX-ray2.15A/B/C/D/E/F2-138[»]
ProteinModelPortalQ9Y239.
SMRQ9Y239. Positions 9-106, 650-951.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid115664. 21 interactions.
DIPDIP-41064N.
IntActQ9Y239. 3 interactions.
MINTMINT-90728.
STRING9606.ENSP00000222823.

Chemistry

BindingDBQ9Y239.
ChEMBLCHEMBL1293222.
GuidetoPHARMACOLOGY1762.

PTM databases

PhosphoSiteQ9Y239.

Polymorphism databases

DMDM20137579.

Proteomic databases

PaxDbQ9Y239.
PRIDEQ9Y239.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000222823; ENSP00000222823; ENSG00000106100.
GeneID10392.
KEGGhsa:10392.
UCSCuc003tav.3. human.

Organism-specific databases

CTD10392.
GeneCardsGC07M030464.
HGNCHGNC:16390. NOD1.
MIM605980. gene.
neXtProtNX_Q9Y239.
PharmGKBPA162398098.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG275503.
HOGENOMHOG000113813.
HOVERGENHBG050793.
InParanoidQ9Y239.
KOK08727.
OMALCYAQKE.
OrthoDBEOG7H4DV9.
PhylomeDBQ9Y239.
TreeFamTF352118.

Enzyme and pathway databases

ReactomeREACT_6782. TRAF6 Mediated Induction of proinflammatory cytokines.
REACT_6900. Immune System.
SignaLinkQ9Y239.

Gene expression databases

ArrayExpressQ9Y239.
BgeeQ9Y239.
CleanExHS_NOD1.
GenevestigatorQ9Y239.

Family and domain databases

Gene3D1.10.533.10. 1 hit.
InterProIPR001315. CARD.
IPR011029. DEATH-like_dom.
IPR007111. NACHT_NTPase.
[Graphical view]
PfamPF00619. CARD. 1 hit.
[Graphical view]
SUPFAMSSF47986. SSF47986. 1 hit.
PROSITEPS50209. CARD. 1 hit.
PS50837. NACHT. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9Y239.
GeneWikiNOD1.
GenomeRNAi10392.
NextBio39370.
PROQ9Y239.
SOURCESearch...

Entry information

Entry nameNOD1_HUMAN
AccessionPrimary (citable) accession number: Q9Y239
Secondary accession number(s): Q549U4, Q8IWF5
Entry history
Integrated into UniProtKB/Swiss-Prot: January 31, 2002
Last sequence update: November 1, 1999
Last modified: April 16, 2014
This is version 140 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 7

Human chromosome 7: entries, gene names and cross-references to MIM