LDB1_XENLA
ID LDB1_XENLA Reviewed; 375 AA.
AC P70060; Q1EQW8; Q7ZXZ7;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 2.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=LIM domain-binding protein 1;
DE Short=LDB-1;
DE Short=xLdb1;
GN Name=ldb1;
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM A), FUNCTION, INTERACTION WITH LHX1,
RP SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC TISSUE=Gastrula;
RX PubMed=8918878; DOI=10.1038/384270a0;
RA Agulnick A.D., Taira M., Breen J.J., Tanaka T., Dawid I.B., Westphal H.;
RT "Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain
RT proteins.";
RL Nature 384:270-272(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM B), ALTERNATIVE SPLICING, TISSUE
RP SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC TISSUE=Brain;
RX PubMed=16815859; DOI=10.1093/jb/mvj134;
RA Tran Y.H., Xu Z., Kato A., Mistry A.C., Goya Y., Taira M., Brandt S.J.,
RA Hirose S.;
RT "Spliced isoforms of LIM-domain-binding protein (CLIM/NLI/Ldb) lacking the
RT LIM-interaction domain.";
RL J. Biochem. 140:105-119(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM A).
RC TISSUE=Embryo;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP INTERACTION WITH LHX1, AND HOMODIMERIZATION.
RX PubMed=9468533; DOI=10.1074/jbc.273.8.4712;
RA Breen J.J., Agulnick A.D., Westphal H., Dawid I.B.;
RT "Interactions between LIM domains and the LIM domain-binding protein
RT Ldb1.";
RL J. Biol. Chem. 273:4712-4717(1998).
RN [5]
RP FUNCTION.
RX PubMed=10926781; DOI=10.1006/dbio.2000.9778;
RA Mochizuki T., Karavanov A.A., Curtiss P.E., Ault K.T., Sugimoto N.,
RA Watabe T., Shiokawa K., Jamrich M., Cho K.W.Y., Dawid I.B., Taira M.;
RT "Xlim-1 and LIM domain binding protein 1 cooperate with various
RT transcription factors in the regulation of the goosecoid promoter.";
RL Dev. Biol. 224:470-485(2000).
RN [6]
RP TISSUE SPECIFICITY.
RX PubMed=11112328; DOI=10.1006/dbio.2000.9951;
RA Chan T.-C., Takahashi S., Asashima M.;
RT "A role for Xlim-1 in pronephros development in Xenopus laevis.";
RL Dev. Biol. 228:256-269(2000).
RN [7]
RP FUNCTION.
RX PubMed=12381786; DOI=10.1073/pnas.212532399;
RA Chen L., Segal D., Hukriede N.A., Podtelejnikov A.V., Bayarsaihan D.,
RA Kennison J.A., Ogryzko V.V., Dawid I.B., Westphal H.;
RT "Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to
RT regulate development.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:14320-14325(2002).
RN [8]
RP INTERACTION WITH LHX1; LHX3; LHX5 AND RNF12, HOMODIMERIZATION, TISSUE
RP SPECIFICITY, AND DEGRADATION BY RNF12.
RX PubMed=12874135; DOI=10.1242/dev.00621;
RA Hiratani I., Yamamoto N., Mochizuki T., Ohmori S.-Y., Taira M.;
RT "Selective degradation of excess Ldb1 by Rnf12/RLIM confers proper Ldb1
RT expression levels and Xlim-1/Ldb1 stoichiometry in Xenopus organizer
RT functions.";
RL Development 130:4161-4175(2003).
CC -!- FUNCTION: Binds to the LIM domain of a wide variety of LIM domain-
CC containing transcription factors. Acts as a coactivator together with
CC otx2 to stimulate lhx1/lim1-mediated activation of the gsc promoter in
CC the Spemann organizer. Acts synergistically with lhx1/lim1 and ssbp in
CC axis formation. {ECO:0000269|PubMed:10926781,
CC ECO:0000269|PubMed:12381786, ECO:0000269|PubMed:8918878}.
CC -!- SUBUNIT: Forms homodimers and heterodimers. Interacts with the LIM
CC domain of LIM/homeobox factor lhx1/lim1, and with lhx3/lim3 and
CC lhx5/lim5. Activates lhx1/lim1 by binding. The stoichiometry of
CC lhx1/lim1 and ldb1 is important for their function and an excess of
CC ldb1 can inhibit lhx1/lim1 function. When bound to lhx1/lim1, escapes
CC degradation by rnf12. The N-terminus interacts with the N-terminal
CC region of rnf12. {ECO:0000269|PubMed:12874135,
CC ECO:0000269|PubMed:8918878, ECO:0000269|PubMed:9468533}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:8918878}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=a;
CC IsoId=P70060-1; Sequence=Displayed;
CC Name=b;
CC IsoId=P70060-2; Sequence=VSP_027836, VSP_027837;
CC -!- TISSUE SPECIFICITY: Ubiquitously expressed in the early gastrula before
CC localizing to the dorsal region of the vegetal hemisphere, which
CC contains the Spemann organizer. Expressed in the CNS, pronephros and
CC tail bud in neurula and tail-bud stage embryos. Expressed in multiple
CC adult tissues including brain, heart, lung, stomach, intestine, liver,
CC spleen, kidney, ovary, muscle and skin. {ECO:0000269|PubMed:11112328,
CC ECO:0000269|PubMed:12874135, ECO:0000269|PubMed:16815859,
CC ECO:0000269|PubMed:8918878}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically during
CC embryogenesis. {ECO:0000269|PubMed:16815859}.
CC -!- DOMAIN: The dimerization domain is located in the N-terminus.
CC {ECO:0000250}.
CC -!- PTM: Undergoes rnf12-mediated ubiquitin-proteasome-dependent
CC degradation.
CC -!- MISCELLANEOUS: [Isoform b]: Lacks LIM-binding domain. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the LDB family. {ECO:0000305}.
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DR EMBL; U74360; AAC60054.1; -; mRNA.
DR EMBL; AB250387; BAE95405.2; -; mRNA.
DR EMBL; BC044043; AAH44043.1; -; mRNA.
DR RefSeq; NP_001080549.1; NM_001087080.1. [P70060-1]
DR RefSeq; NP_001090450.1; NM_001096981.1.
DR RefSeq; XP_018079804.1; XM_018224315.1. [P70060-1]
DR RefSeq; XP_018082552.1; XM_018227063.1.
DR PDB; 6S9S; X-ray; 2.20 A; A=20-200.
DR PDB; 6S9T; X-ray; 2.05 A; A=20-200.
DR PDBsum; 6S9S; -.
DR PDBsum; 6S9T; -.
DR AlphaFoldDB; P70060; -.
DR SMR; P70060; -.
DR DNASU; 380241; -.
DR GeneID; 380241; -.
DR GeneID; 779363; -.
DR KEGG; xla:380241; -.
DR KEGG; xla:779363; -.
DR CTD; 380241; -.
DR CTD; 779363; -.
DR Xenbase; XB-GENE-866237; ldb1.L.
DR Xenbase; XB-GENE-17336783; ldb1.S.
DR OMA; KMSVGCA; -.
DR OrthoDB; 849287at2759; -.
DR Proteomes; UP000186698; Chromosome 7L.
DR Proteomes; UP000186698; Chromosome 7S.
DR Bgee; 380241; Expressed in gastrula and 19 other tissues.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0140297; F:DNA-binding transcription factor binding; IPI:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IPI:UniProtKB.
DR GO; GO:0030274; F:LIM domain binding; IPI:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0003712; F:transcription coregulator activity; IEA:InterPro.
DR GO; GO:0001221; F:transcription coregulator binding; IPI:UniProtKB.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:UniProtKB.
DR InterPro; IPR030167; LDB1.
DR InterPro; IPR041363; LID.
DR InterPro; IPR029005; LIM-bd/SEUSS.
DR PANTHER; PTHR10378; PTHR10378; 1.
DR PANTHER; PTHR10378:SF7; PTHR10378:SF7; 1.
DR Pfam; PF17916; LID; 1.
DR Pfam; PF01803; LIM_bind; 2.
DR PROSITE; PS51957; LID; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Developmental protein; Nucleus;
KW Reference proteome.
FT CHAIN 1..375
FT /note="LIM domain-binding protein 1"
FT /id="PRO_0000084386"
FT DOMAIN 300..339
FT /note="LIM interaction domain (LID)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01302"
FT REGION 248..294
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 331..375
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 267..294
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 338..375
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 300..304
FT /note="DVMVV -> ASASP (in isoform b)"
FT /evidence="ECO:0000303|PubMed:16815859"
FT /id="VSP_027836"
FT VAR_SEQ 305..375
FT /note="Missing (in isoform b)"
FT /evidence="ECO:0000303|PubMed:16815859"
FT /id="VSP_027837"
FT CONFLICT 258
FT /note="S -> N (in Ref. 1; AAC60054)"
FT /evidence="ECO:0000305"
FT HELIX 32..42
FT /evidence="ECO:0007829|PDB:6S9T"
FT HELIX 51..61
FT /evidence="ECO:0007829|PDB:6S9T"
FT STRAND 62..71
FT /evidence="ECO:0007829|PDB:6S9T"
FT STRAND 80..84
FT /evidence="ECO:0007829|PDB:6S9T"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:6S9T"
FT HELIX 88..97
FT /evidence="ECO:0007829|PDB:6S9T"
FT STRAND 100..107
FT /evidence="ECO:0007829|PDB:6S9T"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:6S9T"
FT STRAND 116..132
FT /evidence="ECO:0007829|PDB:6S9T"
FT TURN 134..136
FT /evidence="ECO:0007829|PDB:6S9T"
FT STRAND 139..151
FT /evidence="ECO:0007829|PDB:6S9T"
FT TURN 152..156
FT /evidence="ECO:0007829|PDB:6S9T"
FT STRAND 158..171
FT /evidence="ECO:0007829|PDB:6S9T"
FT HELIX 174..179
FT /evidence="ECO:0007829|PDB:6S9T"
FT TURN 180..182
FT /evidence="ECO:0007829|PDB:6S9T"
FT HELIX 184..191
FT /evidence="ECO:0007829|PDB:6S9T"
SQ SEQUENCE 375 AA; 42825 MW; 1500D3D3698FEB81 CRC64;
MLDRDVGPTP MYPPTYLEPG IGRHTPYGNQ TDYRIFELNK RLQNWTEECD NLWWDAFTTE
FFEDDAMLTI TFCLEDGPKR YTIGRTLIPR YFRSIFEGGA TELYYVLKHP KESFHNNFVS
LDCDQCTMVT QHGKPMFTQV CVEGRLYLEF MFDDMMRIKT WHFSIRQHRE LIPRSILAMH
AQDPQMLDQL SKNITRCGLS NSTLNYLRLC VILEPMQELM SRHKTYSLSP RDCLKTCLFQ
KWQRMVAPPA EPARQAPSKR RKRKMSGGST MSSGGGNTNN SNSKKKSPAS TFALSSQVPD
VMVVGEPTLM GGEFGDEDER LITRLENTQF DAANGIDDED SFNNSPALGA NSPWNSKPPS
SQESKSENPT SQASQ
