LIMD1_HUMAN - dbPTM
LIMD1_HUMAN - PTM Information in dbPTM
Basic Information of Protein
UniProt ID LIMD1_HUMAN
UniProt AC Q9UGP4
Protein Name LIM domain-containing protein 1
Gene Name LIMD1
Organism Homo sapiens (Human).
Sequence Length 676
Subcellular Localization Cytoplasm. Nucleus. Cytoplasm, P-body. Cell junction, adherens junction. Cell junction, focal adhesion. Shuttles between cytoplasm and nucleus but is localized predominantly to the cytoplasm. Found in the nucleus but not nucleoli. Colocalizes with VC
Protein Description Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation..
Protein Sequence MDKYDDLGLEASKFIEDLNMYEASKDGLFRVDKGAGNNPEFEETRRVFATKMAKIHLQQQQQQLLQEETLPRGSRGPVNGGGRLGPQARWEVVGSKLTVDGAAKPPLAASTGAPGAVTTLAAGQPPYPPQEQRSRPYLHGTRHGSQDCGSRESLATSEMSAFHQPGPCEDPSCLTHGDYYDNLSLASPKWGDKPGVSPSIGLSVGSGWPSSPGSDPPLPKPCGDHPLNHRQLSLSSSRSSEGSLGGQNSGIGGRSSEKPTGLWSTASSQRVSPGLPSPNLENGAPAVGPVQPRTPSVSAPLALSCPRQGGLPRSNSGLGGEVSGVMSKPNVDPQPWFQDGPKSYLSSSAPSSSPAGLDGSQQGAVPGLGPKPGCTDLGTGPKLSPTSLVHPVMSTLPELSCKEGPLGWSSDGSLGSVLLDSPSSPRVRLPCQPLVPGPELRPSAAELKLEALTQRLEREMDAHPKADYFGACVKCSKGVFGAGQACQAMGNLYHDTCFTCAACSRKLRGKAFYFVNGKVFCEEDFLYSGFQQSADRCFLCGHLIMDMILQALGKSYHPGCFRCVICNECLDGVPFTVDSENKIYCVRDYHKVLAPKCAACGLPILPPEGSDETIRVVSMDRDYHVECYHCEDCGLELNDEDGHRCYPLEDHLFCHSCHVKRLEKRPSSTALHQHHF
Overview of Protein Modification Sites with Functional and Structural Information
Experimental Post-Translational Modification Sites

* ASA = Accessible Surface Area

Locations Modification Substrate Peptides
&
Secondary Structure		 ASA (%) Reference Orthologous
Protein Cluster
4Phosphorylation----MDKYDDLGLEA
----CCHHHHHHHHH		15.4927642862
12PhosphorylationDDLGLEASKFIEDLN
HHHHHHHHHHHHHHH		20.80-
21PhosphorylationFIEDLNMYEASKDGL
HHHHHHCHHHCCCCC		13.7921945579
24PhosphorylationDLNMYEASKDGLFRV
HHHCHHHCCCCCEEE		21.2421945579
25UbiquitinationLNMYEASKDGLFRVD
HHCHHHCCCCCEEEC		63.9629967540
33UbiquitinationDGLFRVDKGAGNNPE
CCCEEECCCCCCCHH		48.0429967540
51AcetylationTRRVFATKMAKIHLQ
HHHHHHHHHHHHHHH		33.1725953088
51UbiquitinationTRRVFATKMAKIHLQ
HHHHHHHHHHHHHHH		33.1729967540
54UbiquitinationVFATKMAKIHLQQQQ
HHHHHHHHHHHHHHH		27.4529967540
69PhosphorylationQQLLQEETLPRGSRG
HHHHHHCCCCCCCCC		41.1125849741
72MethylationLQEETLPRGSRGPVN
HHHCCCCCCCCCCCC		59.85115482115
75MethylationETLPRGSRGPVNGGG
CCCCCCCCCCCCCCC		57.15115482107
134PhosphorylationYPPQEQRSRPYLHGT
CCCHHHCCCCCCCCC		36.9824719451
135MethylationPPQEQRSRPYLHGTR
CCHHHCCCCCCCCCC		26.52115482123
137PhosphorylationQEQRSRPYLHGTRHG
HHHCCCCCCCCCCCC		15.3824719451
145PhosphorylationLHGTRHGSQDCGSRE
CCCCCCCCCCCCCHH		19.4026329039
150PhosphorylationHGSQDCGSRESLATS
CCCCCCCCHHHHCHH		38.9230242111
153PhosphorylationQDCGSRESLATSEMS
CCCCCHHHHCHHHCC		23.3827080861
156PhosphorylationGSRESLATSEMSAFH
CCHHHHCHHHCCCCC		30.4327080861
157PhosphorylationSRESLATSEMSAFHQ
CHHHHCHHHCCCCCC		26.2027080861
160PhosphorylationSLATSEMSAFHQPGP
HHCHHHCCCCCCCCC		24.5927080861
172PhosphorylationPGPCEDPSCLTHGDY
CCCCCCCHHCCCCCC		33.8023401153
175PhosphorylationCEDPSCLTHGDYYDN
CCCCHHCCCCCCCCC		28.3026356563
179PhosphorylationSCLTHGDYYDNLSLA
HHCCCCCCCCCCCCC		19.8128348404
180PhosphorylationCLTHGDYYDNLSLAS
HCCCCCCCCCCCCCC		11.7721609022
184PhosphorylationGDYYDNLSLASPKWG
CCCCCCCCCCCCCCC		28.3023401153
187PhosphorylationYDNLSLASPKWGDKP
CCCCCCCCCCCCCCC		32.1028464451
197PhosphorylationWGDKPGVSPSIGLSV
CCCCCCCCCCCCEEE		20.8825850435
199PhosphorylationDKPGVSPSIGLSVGS
CCCCCCCCCCEEECC		23.0625850435
203PhosphorylationVSPSIGLSVGSGWPS
CCCCCCEEECCCCCC		21.1526074081
206PhosphorylationSIGLSVGSGWPSSPG
CCCEEECCCCCCCCC		35.2125850435
210PhosphorylationSVGSGWPSSPGSDPP
EECCCCCCCCCCCCC		42.5325159151
211PhosphorylationVGSGWPSSPGSDPPL
ECCCCCCCCCCCCCC		29.2427050516
214PhosphorylationGWPSSPGSDPPLPKP
CCCCCCCCCCCCCCC		50.7825159151
233PhosphorylationPLNHRQLSLSSSRSS
CCCCCEEECCCCCCC		20.1923401153
235PhosphorylationNHRQLSLSSSRSSEG
CCCEEECCCCCCCCC		23.9230266825
236PhosphorylationHRQLSLSSSRSSEGS
CCEEECCCCCCCCCC		34.7630576142
237O-linked_GlycosylationRQLSLSSSRSSEGSL
CEEECCCCCCCCCCC		32.5730059200
237PhosphorylationRQLSLSSSRSSEGSL
CEEECCCCCCCCCCC		32.5724702127
239PhosphorylationLSLSSSRSSEGSLGG
EECCCCCCCCCCCCC		34.3923927012
240PhosphorylationSLSSSRSSEGSLGGQ
ECCCCCCCCCCCCCC		44.8825159151
243PhosphorylationSSRSSEGSLGGQNSG
CCCCCCCCCCCCCCC		21.5725159151
249PhosphorylationGSLGGQNSGIGGRSS
CCCCCCCCCCCCCCC		24.7325332170
255PhosphorylationNSGIGGRSSEKPTGL
CCCCCCCCCCCCCCC		46.2325159151
256PhosphorylationSGIGGRSSEKPTGLW
CCCCCCCCCCCCCCC		48.5620068231
258AcetylationIGGRSSEKPTGLWST
CCCCCCCCCCCCCCC		50.2326051181
260PhosphorylationGRSSEKPTGLWSTAS
CCCCCCCCCCCCCCC		56.8520068231
264PhosphorylationEKPTGLWSTASSQRV
CCCCCCCCCCCCCCC		21.0926074081
265PhosphorylationKPTGLWSTASSQRVS
CCCCCCCCCCCCCCC		20.9826074081
267PhosphorylationTGLWSTASSQRVSPG
CCCCCCCCCCCCCCC		27.3926074081
268PhosphorylationGLWSTASSQRVSPGL
CCCCCCCCCCCCCCC		21.3826074081
272PhosphorylationTASSQRVSPGLPSPN
CCCCCCCCCCCCCCC		18.5529255136
277PhosphorylationRVSPGLPSPNLENGA
CCCCCCCCCCCCCCC		31.3129255136
294PhosphorylationVGPVQPRTPSVSAPL
CCCCCCCCCCCCCCE		26.9725159151
296PhosphorylationPVQPRTPSVSAPLAL
CCCCCCCCCCCCEEC		28.2625159151
298O-linked_GlycosylationQPRTPSVSAPLALSC
CCCCCCCCCCEECCC		28.6230059200
298PhosphorylationQPRTPSVSAPLALSC
CCCCCCCCCCEECCC		28.6221815630
304O-linked_GlycosylationVSAPLALSCPRQGGL
CCCCEECCCCCCCCC		19.2330059200
304PhosphorylationVSAPLALSCPRQGGL
CCCCEECCCCCCCCC		19.2325159151
314PhosphorylationRQGGLPRSNSGLGGE
CCCCCCCCCCCCCCC		33.1529255136
316PhosphorylationGGLPRSNSGLGGEVS
CCCCCCCCCCCCCCE		36.3229255136
323PhosphorylationSGLGGEVSGVMSKPN
CCCCCCCEECCCCCC		22.7429978859
327PhosphorylationGEVSGVMSKPNVDPQ
CCCEECCCCCCCCCC		42.4229978859
343PhosphorylationWFQDGPKSYLSSSAP
CCCCCCHHHHCCCCC		34.1425850435
344PhosphorylationFQDGPKSYLSSSAPS
CCCCCHHHHCCCCCC		19.4126074081
346PhosphorylationDGPKSYLSSSAPSSS
CCCHHHHCCCCCCCC		17.6425850435
347PhosphorylationGPKSYLSSSAPSSSP
CCHHHHCCCCCCCCC		28.1125850435
348PhosphorylationPKSYLSSSAPSSSPA
CHHHHCCCCCCCCCC		40.6025850435
351PhosphorylationYLSSSAPSSSPAGLD
HHCCCCCCCCCCCCC		43.0725850435
352PhosphorylationLSSSAPSSSPAGLDG
HCCCCCCCCCCCCCC		39.0025850435
353PhosphorylationSSSAPSSSPAGLDGS
CCCCCCCCCCCCCCC		24.0925850435
360PhosphorylationSPAGLDGSQQGAVPG
CCCCCCCCCCCCCCC		20.9929978859
371UbiquitinationAVPGLGPKPGCTDLG
CCCCCCCCCCCCCCC		52.8529967540
375PhosphorylationLGPKPGCTDLGTGPK
CCCCCCCCCCCCCCC		39.9329978859
379PhosphorylationPGCTDLGTGPKLSPT
CCCCCCCCCCCCCCH		58.5729978859
384PhosphorylationLGTGPKLSPTSLVHP
CCCCCCCCCHHHHCC		32.0529255136
386PhosphorylationTGPKLSPTSLVHPVM
CCCCCCCHHHHCCHH		31.1729255136
387PhosphorylationGPKLSPTSLVHPVMS
CCCCCCHHHHCCHHH		31.6029255136
394PhosphorylationSLVHPVMSTLPELSC
HHHCCHHHCCCCCCC		27.3329632367
395PhosphorylationLVHPVMSTLPELSCK
HHCCHHHCCCCCCCC		28.3929632367
400PhosphorylationMSTLPELSCKEGPLG
HHCCCCCCCCCCCCC		22.8328060719
409PhosphorylationKEGPLGWSSDGSLGS
CCCCCCCCCCCCCCC		19.4323403867
410PhosphorylationEGPLGWSSDGSLGSV
CCCCCCCCCCCCCCE		39.2123403867
413PhosphorylationLGWSSDGSLGSVLLD
CCCCCCCCCCCEECC		34.2523403867
416PhosphorylationSSDGSLGSVLLDSPS
CCCCCCCCEECCCCC		18.1923663014
421PhosphorylationLGSVLLDSPSSPRVR
CCCEECCCCCCCCCC		27.0125159151
423PhosphorylationSVLLDSPSSPRVRLP
CEECCCCCCCCCCCC		57.8525159151
424PhosphorylationVLLDSPSSPRVRLPC
EECCCCCCCCCCCCC		21.8025159151
428MethylationSPSSPRVRLPCQPLV
CCCCCCCCCCCCCCC		33.9080702705
441MethylationLVPGPELRPSAAELK
CCCCCCCCCCHHHHH		22.82115482131
448UbiquitinationRPSAAELKLEALTQR
CCCHHHHHHHHHHHH		35.4729967540
468PhosphorylationDAHPKADYFGACVKC
HCCCCCCCCHHEEEC		14.5829978859
513PhosphorylationKLRGKAFYFVNGKVF
HHCCCEEEEECCEEE		16.1025159151
527PhosphorylationFCEEDFLYSGFQQSA
EEHHHCCCCCHHHHH		13.5229978859
528PhosphorylationCEEDFLYSGFQQSAD
EHHHCCCCCHHHHHH		34.9729978859
591UbiquitinationYCVRDYHKVLAPKCA
EEEEEHHHHHCCCCH		32.4933845483
656PhosphorylationEDHLFCHSCHVKRLE
CCCEEEEHHHHEHHC		13.7027080861
664UbiquitinationCHVKRLEKRPSSTAL
HHHEHHCCCCCCCCC		74.3629967540
667PhosphorylationKRLEKRPSSTALHQH
EHHCCCCCCCCCCCC		44.3330576142
668PhosphorylationRLEKRPSSTALHQHH
HHCCCCCCCCCCCCC		22.0025850435
669PhosphorylationLEKRPSSTALHQHHF
HCCCCCCCCCCCCCC		37.2630576142
Upstream regulatory proteins (kinases for phosphorylation sites, E3 ubiquitin ligases of ubiquitination sites, ...)
Modified Location Modified Residue Modification Type of Upstream Proteins Gene Name of Upstream Proteins UniProt AC of Upstream Proteins Sources
272SPhosphorylationKinaseCDK1P06493
PSP
272SPhosphorylationKinaseJNK1P45983
PSP
272SPhosphorylationKinaseJNK2P45984
PSP
277SPhosphorylationKinaseCDK1P06493
PSP
277SPhosphorylationKinaseJNK1P45983
PSP
277SPhosphorylationKinaseJNK2P45984
PSP
421SPhosphorylationKinaseCDK1P06493
PSP
421SPhosphorylationKinaseJNK1P45983
PSP
421SPhosphorylationKinaseJNK2P45984
PSP
424SPhosphorylationKinaseCDK1P06493
PSP
424SPhosphorylationKinaseJNK1P45983
PSP
424SPhosphorylationKinaseJNK2P45984
PSP
Functions of PTM Sites
Modified Location Modified Residue Modification Function Reference

Oops, there are no descriptions of PTM sites of LIMD1_HUMAN !!
Disease-associated PTM Sites based on SAP

* Distance = the distance between SAP position and PTM sites.

Modified Location Modification Variant Position
(Distance <= 10) 		Residue Change SAP Related Disease Reference

Oops, there are no SNP-PTM records of LIMD1_HUMAN !!
Protein-Protein Interaction
Interacting Protein Gene Name Interaction Type PPI Reference Domain-Domain Interactions
EGLN2_HUMANEGLN2physical
22286099
EGLN1_HUMANEGLN1physical
22286099
EGLN3_HUMANEGLN3physical
22286099
VHL_HUMANVHLphysical
22286099
A4_HUMANAPPphysical
21832049
TRAF6_HUMANTRAF6physical
17092936
LIMD1_HUMANLIMD1physical
26215701
RHBT3_HUMANRHOBTB3physical
26215701
EGLN1_HUMANEGLN1physical
26215701
VHL_HUMANVHLphysical
26215701
Drug and Disease Associations
Kegg Disease
There are no disease associations of PTM sites.
OMIM Disease
There are no disease associations of PTM sites.
Kegg Drug
There are no disease associations of PTM sites.
DrugBank
There are no disease associations of PTM sites.
Regulatory Network of LIMD1_HUMAN

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Related Literatures of Post-Translational Modification
Phosphorylation
ReferencePubMed
"Quantitative phosphoproteomic analysis of T cell receptor signalingreveals system-wide modulation of protein-protein interactions.";
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,Rodionov V., Han D.K.;
Sci. Signal. 2:RA46-RA46(2009).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-272 AND SER-424, ANDMASS SPECTROMETRY.
"Lys-N and trypsin cover complementary parts of the phosphoproteome ina refined SCX-based approach.";
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,Mohammed S.;
Anal. Chem. 81:4493-4501(2009).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-243, AND MASSSPECTROMETRY.
"A quantitative atlas of mitotic phosphorylation.";
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,Elledge S.J., Gygi S.P.;
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-272; SER-277; SER-296;SER-304; SER-421 AND SER-424, AND MASS SPECTROMETRY.
"Combining protein-based IMAC, peptide-based IMAC, and MudPIT forefficient phosphoproteomic analysis.";
Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D.,Yates J.R. III;
J. Proteome Res. 7:1346-1351(2008).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-304, AND MASSSPECTROMETRY.
"Robust phosphoproteomic profiling of tyrosine phosphorylation sitesfrom human T cells using immobilized metal affinity chromatography andtandem mass spectrometry.";
Brill L.M., Salomon A.R., Ficarro S.B., Mukherji M., Stettler-Gill M.,Peters E.C.;
Anal. Chem. 76:2763-2772(2004).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-272 AND SER-277, ANDMASS SPECTROMETRY.
"An extensive survey of tyrosine phosphorylation revealing new sitesin human mammary epithelial cells.";
Heibeck T.H., Ding S.-J., Opresko L.K., Zhao R., Schepmoes A.A.,Yang F., Tolmachev A.V., Monroe M.E., Camp D.G. II, Smith R.D.,Wiley H.S., Qian W.-J.;
J. Proteome Res. 8:3852-3861(2009).
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-179, AND MASSSPECTROMETRY.

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