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Entry version 149 (18 Sep 2019)
Sequence version 1 (01 Nov 1996)
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Protein

DNA damage checkpoint protein LCD1

Gene

LCD1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Forms a complex with the serine/threonine kinase MEC1 which activates checkpoint signaling upon genotoxic stresses. The MEC1-LCD1 complex is recruited by the single-strand-binding protein complex RPA to DNA lesions in order to initiate the DNA repair by homologous recombination, after the MRX-complex and TEL1 are displaced. Required for the recruitment of MEC1 to DNA lesions, the activation of CHK1 and RAD53 kinases and phosphorylation of RAD9 in response to DNA damage. Required for cell growth and meiotic recombination.9 Publications

Miscellaneous

Present with 606 molecules/cell in log phase SD medium.1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • damaged DNA binding Source: SGD

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionChromatin regulator
Biological processDNA damage, DNA repair

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
YEAST:G3O-30022-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA damage checkpoint protein LCD1
Alternative name(s):
DNA damage checkpoint protein 2
Lethal, checkpoint-defective, DNA damage-sensitive protein 1
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:LCD1
Synonyms:DDC2, PIE1
Ordered Locus Names:YDR499W
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri559292 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002311 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome IV

Organism-specific databases

Eukaryotic Pathogen Database Resources

More...
EuPathDBi
FungiDB:YDR499W

Saccharomyces Genome Database

More...
SGDi
S000002907 LCD1

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi177K → A: Impairs dsDNA and ssDNA binding of the MEC1-LCD1 complex. 1 Publication1
Mutagenesisi179R → A: Impairs dsDNA and ssDNA binding of the MEC1-LCD1 complex. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002277151 – 747DNA damage checkpoint protein LCD1Add BLAST747

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei10PhosphoserineCombined sources1
Modified residuei11PhosphoserineCombined sources1
Modified residuei76PhosphoserineCombined sources1

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Phosphorylated by MEC1 in a cell cycle dependent manner and in response to DNA damage.3 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQB - The MaxQuant DataBase

More...
MaxQBi
Q04377

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q04377

PRoteomics IDEntifications database

More...
PRIDEi
Q04377

PTM databases

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
Q04377

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Forms a complex with MEC1.

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
32550, 60 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...
ComplexPortali
CPX-3621 ATR-ATRIP DNA damage-sensing kinase complex

Database of interacting proteins

More...
DIPi
DIP-2970N

Protein interaction database and analysis system

More...
IntActi
Q04377, 18 interactors

Molecular INTeraction database

More...
MINTi
Q04377

STRING: functional protein association networks

More...
STRINGi
4932.YDR499W

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1747
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q04377

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and domains’ section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>Coiled coili62 – 139Sequence analysisAdd BLAST78

Keywords - Domaini

Coiled coil

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000057105

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q04377

KEGG Orthology (KO)

More...
KOi
K12578

Identification of Orthologs from Complete Genome Data

More...
OMAi
IFQYELI

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR018622 DNA_damage_chkpnt_Lcd1

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF09798 LCD1, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q04377-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRRETVGEFS SDDDDDILLE LGTRPPRFTQ IPPSSAALQT QIPTTLEVTT
60 70 80 90 100
TTLNNKQSKN DNQLVNQLNK AQGEASMLRD KINFLNIERE KEKNIQAVKV
110 120 130 140 150
NELQVKHLQE LAKLKQELQK LEDEKKFLQM EARGKSKREV ITNVKPPSTT
160 170 180 190 200
LSTNTNTITP DSSSVAIEAK PQSPQSKKRK ISDNLLKKNM VPLNPNRIIP
210 220 230 240 250
DETSLFLESI LLHQIIGADL STIEILNRLK LDYITEFKFK NFVIAKGAPI
260 270 280 290 300
GKSIVSLLLR CKKTLTLDRF IDTLLEDIAV LIKEISVHPN ESKLAVPFLV
310 320 330 340 350
ALMYQIVQFR PSATHNLALK DCFLFICDLI RIYHHVLKVP IHESNMNLHV
360 370 380 390 400
EPQIFQYELI DYLIISYSFD LLEGILRVLQ SHPKQTYMEF FDENILKSFE
410 420 430 440 450
FVYKLALTIS YKPMVNVIFS AVEVVNIITS IILNMDNSSD LKSLISGSWW
460 470 480 490 500
RDCITRLYAL LEKEIKSGDV YNENVDTTTL HMSKYHDFFG LIRNIGDNEL
510 520 530 540 550
GGLISKLIYT DRLQSVPRVI SKEDIGMDSD KFTAPIIGYK MEKWLLKLKD
560 570 580 590 600
EVLNIFENLL MIYGDDATIV NGEMLIHSSK FLSREQALMI ERYVGQDSPN
610 620 630 640 650
LDLRCHLIEH TLTIIYRLWK DHFKQLREEQ IKQVESQLIM SLWRFLVCQT
660 670 680 690 700
ETVTANEREM RDHRHLVDSL HDLTIKDQAS YYEDAFEDLP EYIEEELKMQ
710 720 730 740
LNKRTGRIMQ VKYDEKFQEM ARTILESKSF DLTTLEEADS LYISMGL
Length:747
Mass (Da):86,425
Last modified:November 1, 1996 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iE981C1A38F3310BF
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U33057 Genomic DNA Translation: AAB64941.1
BK006938 Genomic DNA Translation: DAA12331.1

Protein sequence database of the Protein Information Resource

More...
PIRi
S69557

NCBI Reference Sequences

More...
RefSeqi
NP_010787.3, NM_001180807.3

Genome annotation databases

Ensembl fungal genome annotation project

More...
EnsemblFungii
YDR499W_mRNA; YDR499W; YDR499W

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
852110

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
sce:YDR499W

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U33057 Genomic DNA Translation: AAB64941.1
BK006938 Genomic DNA Translation: DAA12331.1
PIRiS69557
RefSeqiNP_010787.3, NM_001180807.3

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5OMDX-ray2.10A73-136[»]
5X6Oelectron microscopy3.90G1-747[»]
SMRiQ04377
ModBaseiSearch...

Protein-protein interaction databases

BioGridi32550, 60 interactors
ComplexPortaliCPX-3621 ATR-ATRIP DNA damage-sensing kinase complex
DIPiDIP-2970N
IntActiQ04377, 18 interactors
MINTiQ04377
STRINGi4932.YDR499W

PTM databases

iPTMnetiQ04377

Proteomic databases

MaxQBiQ04377
PaxDbiQ04377
PRIDEiQ04377

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYDR499W_mRNA; YDR499W; YDR499W
GeneIDi852110
KEGGisce:YDR499W

Organism-specific databases

EuPathDBiFungiDB:YDR499W
SGDiS000002907 LCD1

Phylogenomic databases

HOGENOMiHOG000057105
InParanoidiQ04377
KOiK12578
OMAiIFQYELI

Enzyme and pathway databases

BioCyciYEAST:G3O-30022-MONOMER

Miscellaneous databases

Protein Ontology

More...
PROi
PR:Q04377

Family and domain databases

InterProiView protein in InterPro
IPR018622 DNA_damage_chkpnt_Lcd1
PfamiView protein in Pfam
PF09798 LCD1, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiLCD1_YEAST
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q04377
Secondary accession number(s): D6VTC1
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: November 1, 1996
Last modified: September 18, 2019
This is version 149 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  2. Yeast chromosome IV
    Yeast (Saccharomyces cerevisiae) chromosome IV: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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