Protein:ERCC5 |
Protein Summary |
 Gene summary |
| Gene name: ERCC5 | ASpdb.0 ID: 2073 | Gene | Gene symbol | ERCC5 | Gene ID | 2073 |
| Gene name | ERCC excision repair 5, endonuclease |
| Synonyms | COFS3|ERCC5-201|ERCM2|UVDR|XPG|XPGC |
| Cytomap | 13q33.1 |
| Type of gene | protein-coding |
| Description | DNA excision repair protein ERCC-5DNA repair protein complementing XP-G cellsXPG-complementing proteinexcision repair cross-complementation group 5excision repair cross-complementing rodent repair deficiency, complementation group 5xeroderma pigmento |
| Modification date | 20240407 |
| UniProtAcc | P28715 |
| Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Gene | ERCC5 | GO:0000109 | nucleotide-excision repair complex | 11259578 |
| Gene | ERCC5 | GO:0000405 | bubble DNA binding | 16246722|32821917 |
| Gene | ERCC5 | GO:0000993 | RNA polymerase II complex binding | 16246722 |
| Gene | ERCC5 | GO:0003684 | damaged DNA binding | 32821917 |
| Gene | ERCC5 | GO:0003690 | double-stranded DNA binding | 8090225|12644470 |
| Gene | ERCC5 | GO:0003697 | single-stranded DNA binding | 12644470 |
| Gene | ERCC5 | GO:0004519 | endonuclease activity | 32522879|32821917 |
| Gene | ERCC5 | GO:0004520 | DNA endonuclease activity | 8090225|12644470 |
| Gene | ERCC5 | GO:0005634 | nucleus | 8710877|26833090 |
| Gene | ERCC5 | GO:0005662 | DNA replication factor A complex | 7700386 |
| Gene | ERCC5 | GO:0006285 | base-excision repair, AP site formation | 9927729 |
| Gene | ERCC5 | GO:0006289 | nucleotide-excision repair | 8090225|11259578|32522879|32821917 |
| Gene | ERCC5 | GO:0008047 | enzyme activator activity | 9927729 |
| Gene | ERCC5 | GO:0009411 | response to UV | 8710877 |
| Gene | ERCC5 | GO:0032991 | protein-containing complex | 26833090 |
| Gene | ERCC5 | GO:0044877 | protein-containing complex binding | 11259578 |
| Gene | ERCC5 | GO:0050790 | regulation of catalytic activity | 9927729 |
AS Summary |
| Information of the canonical protein with experimentally identified structure from PDB (2023). |
| UniProt Acc | File name | PDB ID | Method | Resolution | Chain | Start | End |
| P28715-1 | P28715-1_6tux_A.pdb | 6TUX | X-ray | 3.1 | A | 753 | 986 |
| ASpdb's canonical and alternatively spliced isoform information. |
| accession_id | gene_name | canonical_id | alternative_id | canonical_length | alternative_length | canonical_start | canonical_end | type | originalSEQ | variationSEQ | alternative_start | alternative_end |
| P28715 | ERCC5 | P28715-1 | P28715-2 | 1186 | 419 | 1 | 767 | Deletion | none | none | 0 | 0 |
| P28715 | ERCC5 | P28715-1 | P28715-3 | 1186 | 232 | 225 | 232 | Substitution | ESDDFSQY | VYLPLLQP | 225 | 232 |
| P28715 | ERCC5 | P28715-1 | P28715-3 | 1186 | 232 | 233 | 1186 | Deletion | none | none | 232 | 232 |
| Multiple sequence alignment of our canonical and alternatively spliced ERCC5 |
| Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of ERCC5 |
| UniProt-id | ENSG | ENST | ENSP |
| P28715-1 | ENSG00000134899.24 | ENST00000652225.2 | ENSP00000498881.2 |
| UniProt-id | NM ID | NP ID |
| P28715-1 | NM_000123.3 | NP_000114.2 |
| Amino acid sequences of our canonical and alternatively spliced ERCC5 |
| accession_id | Protein sequence |
| P28715-1 | MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLVK RRQRKDLASSDSRKTTEKLLKTFLKRQAIKTAFRSKRDEALPSLTQVRRENDLYVLPPLQEEEKHSSEEEDEKEWQERMNQKQALQEEFF HNPQAIDIESEDFSSLPPEVKHEILTDMKEFTKRRRTLFEAMPEESDDFSQYQLKGLLKKNYLNQHIEHVQKEMNQQHSGHIRRQYEDEG GFLKEVESRRVVSEDTSHYILIKGIQAKTVAEVDSESLPSSSKMHGMSFDVKSSPCEKLKTEKEPDATPPSPRTLLAMQAALLGSSSEEE LESENRRQARGRNAPAAVDEGSISPRTLSAIKRALDDDEDVKVCAGDDVQTGGPGAEEMRINSSTENSDEGLKVRDGKGIPFTATLASSS VNSAEEHVASTNEGREPTDSVPKEQMSLVHVGTEAFPISDESMIKDRKDRLPLESAVVRHSDAPGLPNGRELTPASPTCTNSVSKNETHA EVLEQQNELCPYESKFDSSLLSSDDETKCKPNSASEVIGPVSLQETSSIVSVPSEAVDNVENVVSFNAKEHENFLETIQEQQTTESAGQD LISIPKAVEPMEIDSEESESDGSFIEVQSVISDEELQAEFPETSKPPSEQGEEELVGTREGEAPAESESLLRDNSERDDVDGEPQEAEKD AEDSLHEWQDINLEELETLESNLLAQQNSLKAQKQQQERIAATVTGQMFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDD SDIWLFGARHVYRNFFNKNKFVEYYQYVDFHNQLGLDRNKLINLAYLLGSDYTEGIPTVGCVTAMEILNEFPGHGLEPLLKFSEWWHEAQ KNPKIRPNPHDTKVKKKLRTLQLTPGFPNPAVAEAYLKPVVDDSKGSFLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLKQLDAQQTQ LRIDSFFRLAQQEKEDAKRIKSQRLNRAVTCMLRKEKEAAASEIEAVSVAMEKEFELLDKAKGKTQKRGITNTLEESSSLKRKRLSDSKG KNTCGGFLGETCLSESSDGSSSEDAESSSLMNVQRRTAAKEPKTSASDSQNSVKEAPVKNGGATTSSSSDSDDDGGKEKMVLVTARSVFG |
| P28715-2 | MFLESQELLRLFGIPYIQAPMEAEAQCAILDLTDQTSGTITDDSDIWLFGARHVYRNFFNKNKFVEYYQYVDFHNQLGLDRNKLINLAYL LGSDYTEGIPTVGCVTAMEILNEFPGHGLEPLLKFSEWWHEAQKNPKIRPNPHDTKVKKKLRTLQLTPGFPNPAVAEAYLKPVVDDSKGS FLWGKPDLDKIREFCQRYFGWNRTKTDESLFPVLKQLDAQQTQLRIDSFFRLAQQEKEDAKRIKSQRLNRAVTCMLRKEKEAAASEIEAV SVAMEKEFELLDKAKGKTQKRGITNTLEESSSLKRKRLSDSKGKNTCGGFLGETCLSESSDGSSSEDAESSSLMNVQRRTAAKEPKTSAS |
| P28715-3 | MGVQGLWKLLECSGRQVSPEALEGKILAVDISIWLNQALKGVRDRHGNSIENPHLLTLFHRLCKLLFFRIRPIFVFDGDAPLLKKQTLVK RRQRKDLASSDSRKTTEKLLKTFLKRQAIKTAFRSKRDEALPSLTQVRRENDLYVLPPLQEEEKHSSEEEDEKEWQERMNQKQALQEEFF |
Protein Functional Features |
| Main function of this protein. (from UniProt) |
| ERCC5 (go to UniProt):P28715 |
| Retention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at * Minus value of BPloci means that the break pointn is located before the CDS. |
| - Retained protein feature among the 13 regional features. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P28715 | Region | 1 | 78 | Note=N-domain;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:32522879;Dbxref=PMID:32522879 | Type=Deletion;Start=1;End=767 |
| P28715 | Region | 31 | 67 | "Note=DNA-binding%3B may bind to the undamaged single-strand DNA of the DNA repair bubble;Ontology_term=ECO:0000269 | ECO:0000312 |
| P28715 | Region | 79 | 785 | Note=Spacer region;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16246722;Dbxref=PMID:16246722 | Type=Deletion;Start=1;End=767 |
| P28715 | Region | 79 | 785 | Note=Spacer region;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16246722;Dbxref=PMID:16246722 | Type=Substitution;Start=225;End=232 |
| P28715 | Region | 79 | 785 | Note=Spacer region;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16246722;Dbxref=PMID:16246722 | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 306 | 342 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=767 |
| P28715 | Region | 306 | 342 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 354 | 385 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=767 |
| P28715 | Region | 354 | 385 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 404 | 473 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=767 |
| P28715 | Region | 404 | 473 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 510 | 533 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=767 |
| P28715 | Region | 510 | 533 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 667 | 724 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=767 |
| P28715 | Region | 667 | 724 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 786 | 881 | Note=I-domain;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:32522879;Dbxref=PMID:32522879 | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 820 | 836 | "Note=DNA-binding%3B may bind to the undamaged single-strand DNA of the DNA repair bubble;Ontology_term=ECO:0000269 | ECO:0000312 |
| P28715 | Region | 848 | 880 | "Note=DNA-binding%3B H2TH (helix-2turn-helix) motif which binds double-stranded DNA;Ontology_term=ECO:0000269 | ECO:0000312 |
| P28715 | Region | 912 | 918 | "Note=DNA-binding%3B may bind double-stranded DNA;Ontology_term=ECO:0000269 | ECO:0000312 |
| P28715 | Region | 981 | 1009 | Note=Interaction with PCNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9305916;Dbxref=PMID:9305916 | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 1011 | 1186 | Note=Interaction with ERCC6/CSB;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16246722;Dbxref=PMID:16246722 | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 1056 | 1081 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 1095 | 1186 | Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Motif | 1057 | 1074 | Note=Nuclear localization signal 1;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:26812207;Dbxref=PMID:26812207 | Type=Deletion;Start=233;End=1186 |
| P28715 | Motif | 1169 | 1186 | Note=Nuclear localization signal 2;Ontology_term=ECO:0000305;evidence=ECO:0000305|PubMed:26812207;Dbxref=PMID:26812207 | Type=Deletion;Start=233;End=1186 |
| P28715 | Compositional bias | 443 | 458 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=767 |
| P28715 | Compositional bias | 443 | 458 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Compositional bias | 676 | 724 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=1;End=767 |
| P28715 | Compositional bias | 676 | 724 | Note=Basic and acidic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Compositional bias | 1095 | 1150 | Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
| P28715 | Compositional bias | 1168 | 1186 | Note=Basic residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite | Type=Deletion;Start=233;End=1186 |
Gene Isoform Structures and Expression Levels for ERCC5 |
| Gene structures of our canonical and alternative spliced genes of ERCC5 * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Expression levels of gene isoforms across GTEx. |
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| Expression levels of gene isoforms across TCGA. |
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Protein Structures |
| PDB and CIF files of the predicted protein structures * Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format. |
| 3D view using mol* of P28715-1 |
| 3D view using mol* of P28715-2 |
| 3D view using mol* of P28715-3 |
pLDDT Score Distribution |
| pLDDT score distribution of the predicted protein structures from AlphaFold2 * AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. |
| pLDDT distribution across the protein length of P28715-1 |
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| pLDDT distribution across the protein length of P28715-2 |
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| pLDDT distribution across the protein length of P28715-3 |
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Ramachandran Plot of Protein Structures |
| Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide. |
| Ramachandran plot of P28715-1 |
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| Ramachandran plot of P28715-2 |
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Potential Active Site Information |
| The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite. |
| UniProt-id | Site score | Size | D score | Volume | Exposure | Enclosure | Contact | Phobic | Philic | Balance | Don/Acc | Residues |
| P28715-1 | 1.016 | 163 | 0.998 | 596.134 | 0.628 | 0.721 | 0.882 | 0.375 | 1.15 | 0.326 | 0.637 | 1,2,3,4,5,6,7,8,11,30,32,33,36,77,78,79,80,84,85,8 7,88,89,91,92,94,95,96,760,761,763,789,790,791,809 ,810,811,812,816,823,858,859,860,861,863,864,865,9 36 |
| P28715-2 | 1.04 | 171 | 1.094 | 709.667 | 0.671 | 0.686 | 0.812 | 0.833 | 0.789 | 1.055 | 0.998 | 41,42,43,44,47,48,54,56,63,64,65,66,67,68,69,72,73 ,76,77,79,84,87,88,91,104,108,232,233,234,235,236, 240,241,242,243,244,248,249,400,401,402 |
| P28715-3 | 0.879 | 69 | 0.924 | 261.366 | 0.701 | 0.59 | 0.785 | 0.741 | 0.645 | 1.147 | 0.943 | 109,112,113,116,117,120,123,124,127,128,129,130,13 1,132,133,134,136 |
Protein Structure and Feature Comparision |
| Protein Structure Comparision Using Template Modeling Scores (TM-score). |
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| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green) |
| 3D view using mol* of P28715-1_P28715-1_6tux_A.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P28715-1_6tux_A_P28715-2.pdb |
| 3D view using mol* of P28715-1_6tux_A_P28715-3.pdb |
| Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green) |
| 3D view using mol* of P28715-1_P28715-2.pdb |
| 3D view using mol* of P28715-1_P28715-3.pdb |
| Protein Feature Comparison of the protein sequendary structures among the protiens. |
| ./stats/secondary_structure/figure/P28715-1_vs_P28715-2.png |
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| ./stats/secondary_structure/figure/P28715-1_vs_P28715-3.png |
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| Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens. |
| ./stats/relative_asa/P28715-1_vs_P28715-2.png |
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| ./stats/relative_asa/P28715-1_vs_P28715-3.png |
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Protein-Protein Interaction |
| Interactors from UniProt. |
| Accession_id | Subsection | Start | End | Funcitonal feature | Splicing information |
| P28715 | Region | 981 | 1009 | Note=Interaction with PCNA;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9305916;Dbxref=PMID:9305916 | Type=Deletion;Start=233;End=1186 |
| P28715 | Region | 1011 | 1186 | Note=Interaction with ERCC6/CSB;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16246722;Dbxref=PMID:16246722 | Type=Deletion;Start=233;End=1186 |
| Interactors from STRING. |
| Gene name | Interactors |
Related Drugs to ERCC5 |
| Drugs targeting this gene/protein. (DrugBank) |
| UniProt accession | Gene name | DrugBank ID | Drug name | Drug group | Actions |
Related Diseases to ERCC5 |
| Previous studies relating to the alternative splicing of ERCC5 and disease information from the MeSH term (PubMed) |
| Gene | PMID | Title | Abstract | MeSH ID | MeSH term |
| ERCC5 | 11841555 | The founding members of xeroderma pigmentosum group G produce XPG protein with severely impaired endonuclease activity. | Of the eight human genes implicated in xeroderma pigmentosum, defects in XPG produce some of the most clinically diverse symptoms. These range from mild freckling to severe skeletal and neurologic abnormalities characteristic of Cockayne syndrome. Mildly affected xeroderma pigmentosum group G patients have diminished XPG endonuclease activity in nucleotide excision repair, whereas severely affected xeroderma pigmentosum group G/Cockayne syndrome patients produce truncated XPG proteins that are unable to function in either nucleotide excision repair or the transcription-coupled repair of oxidative lesions. The first two xeroderma pigmentosum group G patients, XP2BI and XP3BR, were reported before the relationship between xeroderma pigmentosum group G and Cockayne syndrome was appreciated. Here we provide evidence that both patients produce truncated proteins from one XPG allele. From the second allele, XP2BI generates full-length XPG of 1186 amino acids containing a single L858P substitution that has reduced stability and greatly impaired endonuclease activity. In XP3BR, a single base deletion and alternative splicing at a rare noncanonical AT-AC intron produces a 1185 amino acid protein containing 44 internal non-XPG residues. This protein is stably expressed but it also has greatly impaired endonuclease activity. These four XPG products can thus account for the severe ultraviolet sensitivity of XP2BI and XP3BR fibroblasts. These cells, unlike those from xeroderma pigmentosum group G/Cockayne syndrome patients, are capable of limited transcription-coupled repair of oxidative lesions. Our results suggest that the L858P protein in XP2BI and the almost full-length XPG protein in XP3BR are responsible for this activity and for the absence of severe early onset Cockayne syndrome symptoms in these patients. | D014983 | Xeroderma Pigmentosum |
Clinically important variants in ERCC5 |
| (ClinVar, 04/20/2024) |
| accession_id | uniprot_id | gene_name | Type | Variant | Clinical_significance |
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