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ELAC2 (elaC homolog 2 (E. coli))

Written2008-02Yang Chen, Sean Tavtigian, Donna Shattuck
Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT 84108, USA

(Note : for Links provided by Atlas : click)

Identity

Other namesHPC2
TRZ1 (tRNaseZL)
HGNC (Hugo) ELAC2
LocusID (NCBI) 60528
Atlas_Id 40437
Location 17p12  [Link to chromosome band 17p12]
Location_base_pair Starts at 12894929 and ends at 12921381 bp from pter ( according to hg19-Feb_2009)  [Mapping ELAC2.png]
Local_order Telomeric to HS3ST3A1 and centromeric to KIAA0672.
Fusion genes
(updated 2016)
DLST (14q24.3) / ELAC2 (17p12)ELAC2 (17p12) / COX10 (17p12)RPSAP52 (12q14.3) / ELAC2 (17p12)
Note There is a human paralog of this gene on chromosome 18 called ELAC1 that is homologous to the C-terminal half of ELAC2.

DNA/RNA

Note Ubiquitously expressed in a variety of tissues, tumors and developmental stages.
Description The genomic size of ELAC2 gene is about 25.6 kb representing a mRNA of 2966 bp with 26 exons.
Transcription There is no evidence of alternative splicing of the transcript.
Pseudogene No known pseudogenes.

Protein

Description ELAC2 gene encodes a protein of 826 amino acids. Orthologs are found in Eukaryotes including M. musculus, R. norvegicus, C. elegans, D. melanogaster, S. cerevisiae, S. pombe and A. thaliana.
Expression Not determined.
Localisation Not determined. But is implicated in nucleus upon overexpression in cell lines. Yeast ortholog (TRZ1p) is detected in cytosol, nucleus and mitochondria via large-scale analysis with GFP tagged gene product.
Function ELAC2 has tRNA processing activity as detected by in vitro biochemistry assays. The N-terminus of ELAC2 is required for the Rnase 65 activity. The C-terminus (481-826 aa) of ELAC2, which is homologous to ELAC1, possesses tRNA 3' processing endoribonuclease acitivity (tRNaseZ). Overexpressed ELAC2 binds gamma-tubulin complex and is involved in cell cycle regulation. ELAC2 has also been shown to potentiate TGF-beta-induced growth arrest of prostate cells via over-expression upon transfection and down-regulation via siRNA.

Mutations

Germinal One pedigree-specific insertion/frameshift, 1641insG, resulting in frameshift after L547, and leading to termination after the miscoding of 67 residues. Four missense variants, S217L, A541T, E622V and R781H.
Somatic Not determined.

Implicated in

Note
Entity Prostate Cancer
Note TGF-beta signaling mediated growth arrest via physical interactions with Smad2 / Smad3 and FAST-1, and potentiation of Smad2-driven (ARE)2-Luciferease reporter activity. Also implicated in RNA processing.
Disease Hereditary prostate cancer and sporadic prostate cancer.
  

Bibliography

Characterization of TRZ1, a yeast homolog of the human candidate prostate cancer susceptibility gene ELAC2 encoding tRNase Z.
Chen Y, Beck A, Davenport C, Chen Y, Shattuck D, Tavtigian SV
BMC molecular biology. 2005 ; 6 (1) : page 12.
PMID 15892892
 
Association of common missense changes in ELAC2 ( HPC2) with prostate cancer in a Japanese case-control series.
Fujiwara H, Emi M, Nagai H, Nishimura T, Konishi N, Kubota Y, Ichikawa T, Takahashi S, Shuin T, Habuchi T, Ogawa O, Inoue K, Skolnick MH, Swensen J, Camp NJ, Tavtigian SV
Journal of human genetics. 2002 ; 47 (12) : 641-648.
PMID 12522685
 
Assigning function to yeast proteins by integration of technologies.
Hazbun TR, Malmström L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, Yates JR 3rd, Davis TN
Molecular cell. 2003 ; 12 (6) : 1353-1365.
PMID 14690591
 
Global analysis of protein localization in budding yeast.
Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK
Nature. 2003 ; 425 (6959) : 686-691.
PMID 14562095
 
The product of the candidate prostate cancer susceptibility gene ELAC2 interacts with the gamma-tubulin complex.
Korver W, Guevara C, Chen Y, Neuteboom S, Bookstein R, Tavtigian S, Lees E
International journal of cancer. Journal international du cancer. 2003 ; 104 (3) : 283-288.
PMID 12569551
 
ELAC2, a putative prostate cancer susceptibility gene product, potentiates TGF-beta/Smad-induced growth arrest of prostate cells.
Noda D, Itoh S, Watanabe Y, Inamitsu M, Dennler S, Itoh F, Koike S, Danielpour D, ten Dijke P, Kato M
Oncogene. 2006 ; 25 (41) : 5591-5600.
PMID 16636667
 
ELAC2/HPC2 involvement in hereditary and sporadic prostate cancer.
Rökman A, Ikonen T, Mononen N, Autio V, Matikainen MP, Koivisto PA, Tammela TL, Kallioniemi OP, Schleutker J
Cancer research. 2001 ; 61 (16) : 6038-6041.
PMID 11507049
 
Polymorphisms in the prostate cancer susceptibility gene HPC2/ELAC2 in multiplex families and healthy controls.
Suarez BK, Gerhard DS, Lin J, Haberer B, Nguyen L, Kesterson NK, Catalona WJ
Cancer research. 2001 ; 61 (13) : 4982-4984.
PMID 11431329
 
The N-terminal half-domain of the long form of tRNase Z is required for the RNase 65 activity.
Takaku H, Minagawa A, Takagi M, Nashimoto M
Nucleic acids research. 2004 ; 32 (15) : 4429-4438.
PMID 15317868
 
A candidate prostate cancer susceptibility gene at chromosome 17p.
Tavtigian SV, Simard J, Teng DH, Abtin V, Baumgard M, Beck A, Camp NJ, Carillo AR, Chen Y, Dayananth P, Desrochers M, Dumont M, Farnham JM, Frank D, Frye C, Ghaffari S, Gupte JS, Hu R, Iliev D, Janecki T, Kort EN, Laity KE, Leavitt A, Leblanc G, McArthur-Morrison J, Pederson A, Penn B, Peterson KT, Reid JE, Richards S, Schroeder M, Smith R, Snyder SC, Swedlund B, Swensen J, Thomas A, Tranchant M, Woodland AM, Labrie F, Skolnick MH, Neuhausen S, Rommens J, Cannon-Albright LA
Nature genetics. 2001 ; 27 (2) : 172-180.
PMID 11175785
 
Role of HPC2/ELAC2 in hereditary prostate cancer.
Wang L, McDonnell SK, Elkins DA, Slager SL, Christensen E, Marks AF, Cunningham JM, Peterson BJ, Jacobsen SJ, Cerhan JR, Blute ML, Schaid DJ, Thibodeau SN
Cancer research. 2001 ; 61 (17) : 6494-6499.
PMID 11522646
 

Citation

This paper should be referenced as such :
Chen, Y ; Tavtigian, S ; Shattuck, D. ELAC2 (elaC homolog 2 (E
coli))
Atlas Genet Cytogenet Oncol Haematol. 2008;12(6):430-431.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/ELAC2ID40437ch17p11.html


Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Hereditary prostate cancer

External links

Nomenclature
HGNC (Hugo)ELAC2   14198
Cards
AtlasELAC2ID40437ch17p11
Entrez_Gene (NCBI)ELAC2  60528  elaC ribonuclease Z 2
AliasesCOXPD17; ELC2; HPC2
GeneCards (Weizmann)ELAC2
Ensembl hg19 (Hinxton)ENSG00000006744 [Gene_View]  chr17:12894929-12921381 [Contig_View]  ELAC2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000006744 [Gene_View]  chr17:12894929-12921381 [Contig_View]  ELAC2 [Vega]
ICGC DataPortalENSG00000006744
TCGA cBioPortalELAC2
AceView (NCBI)ELAC2
Genatlas (Paris)ELAC2
WikiGenes60528
SOURCE (Princeton)ELAC2
Genomic and cartography
GoldenPath hg19 (UCSC)ELAC2  -     chr17:12894929-12921381 -  17p11.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)ELAC2  -     17p11.2   [Description]    (hg38-Dec_2013)
EnsemblELAC2 - 17p11.2 [CytoView hg19]  ELAC2 - 17p11.2 [CytoView hg38]
Mapping of homologs : NCBIELAC2 [Mapview hg19]  ELAC2 [Mapview hg38]
OMIM605367   614731   615440   
Gene and transcription
Genbank (Entrez)AA706335 AF304370 AK001392 AK074244 AK094012
RefSeq transcript (Entrez)NM_001165962 NM_018127 NM_173717
RefSeq genomic (Entrez)NC_000017 NC_018928 NG_015808 NT_010718 NW_004929405
Consensus coding sequences : CCDS (NCBI)ELAC2
Cluster EST : UnigeneHs.434232 [ NCBI ]
CGAP (NCI)Hs.434232
Alternative Splicing GalleryENSG00000006744
Gene ExpressionELAC2 [ NCBI-GEO ]   ELAC2 [ EBI - ARRAY_EXPRESS ]   ELAC2 [ SEEK ]   ELAC2 [ MEM ]
Gene Expression Viewer (FireBrowse)ELAC2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)60528
GTEX Portal (Tissue expression)ELAC2
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BQ52 (Uniprot)
NextProtQ9BQ52  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BQ52
Splice isoforms : SwissVarQ9BQ52 (Swissvar)
Catalytic activity : Enzyme3.1.26.11 [ Enzyme-Expasy ]   3.1.26.113.1.26.11 [ IntEnz-EBI ]   3.1.26.11 [ BRENDA ]   3.1.26.11 [ KEGG ]   
PhosPhoSitePlusQ9BQ52
Domains : Interpro (EBI)Metallo-B-lactamas    tRNase_Z_dom   
Domain families : Pfam (Sanger)Lactamase_B_2 (PF12706)    Lactamase_B_4 (PF13691)   
Domain families : Pfam (NCBI)pfam12706    pfam13691   
Domain families : Smart (EMBL)Lactamase_B (SM00849)  
DMDM Disease mutations60528
Blocks (Seattle)ELAC2
SuperfamilyQ9BQ52
Human Protein AtlasENSG00000006744
Peptide AtlasQ9BQ52
HPRD05641
IPIIPI00396627   IPI00398822   IPI00398823   IPI00798145   IPI01011409   IPI00789842   
Protein Interaction databases
DIP (DOE-UCLA)Q9BQ52
IntAct (EBI)Q9BQ52
FunCoupENSG00000006744
BioGRIDELAC2
STRING (EMBL)ELAC2
ZODIACELAC2
Ontologies - Pathways
QuickGOQ9BQ52
Ontology : AmiGOendonuclease activity  tRNA-specific ribonuclease activity  nucleus  nucleoplasm  nucleoplasm  mitochondrion  mitochondrial matrix  mitochondrial nucleoid  tRNA 3'-end processing  poly(A) RNA binding  metal ion binding  mitochondrial tRNA 3'-trailer cleavage, endonucleolytic  mitochondrial tRNA processing  
Ontology : EGO-EBIendonuclease activity  tRNA-specific ribonuclease activity  nucleus  nucleoplasm  nucleoplasm  mitochondrion  mitochondrial matrix  mitochondrial nucleoid  tRNA 3'-end processing  poly(A) RNA binding  metal ion binding  mitochondrial tRNA 3'-trailer cleavage, endonucleolytic  mitochondrial tRNA processing  
Pathways : KEGGRNA transport   
NDEx NetworkELAC2
Atlas of Cancer Signalling NetworkELAC2
Wikipedia pathwaysELAC2
Orthology - Evolution
OrthoDB60528
GeneTree (enSembl)ENSG00000006744
Phylogenetic Trees/Animal Genes : TreeFamELAC2
Homologs : HomoloGeneELAC2
Homology/Alignments : Family Browser (UCSC)ELAC2
Gene fusions - Rearrangements
Fusion: TCGAELAC2 17p12 COX10 17p12 PRAD
Polymorphisms : SNP, variants
NCBI Variation ViewerELAC2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ELAC2
dbVarELAC2
ClinVarELAC2
1000_GenomesELAC2 
Exome Variant ServerELAC2
ExAC (Exome Aggregation Consortium)ELAC2 (select the gene name)
Genetic variants : HAPMAP60528
Genomic Variants (DGV)ELAC2 [DGVbeta]
Mutations
ICGC Data PortalELAC2 
TCGA Data PortalELAC2 
Broad Tumor PortalELAC2
OASIS PortalELAC2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICELAC2 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch ELAC2
DgiDB (Drug Gene Interaction Database)ELAC2
DoCM (Curated mutations)ELAC2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ELAC2 (select a term)
intoGenELAC2
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)17:12894929-12921381  ENSG00000006744
CONAN: Copy Number AnalysisELAC2 
Mutations and Diseases : HGMDELAC2
OMIM605367    614731    615440   
MedgenELAC2
Genetic Testing Registry ELAC2
NextProtQ9BQ52 [Medical]
TSGene60528
GENETestsELAC2
Huge Navigator ELAC2 [HugePedia]
snp3D : Map Gene to Disease60528
BioCentury BCIQELAC2
ClinGenELAC2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD60528
Chemical/Pharm GKB GenePA27739
Clinical trialELAC2
Miscellaneous
canSAR (ICR)ELAC2 (select the gene name)
Probes
Litterature
PubMed63 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineELAC2
EVEXELAC2
GoPubMedELAC2
iHOPELAC2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 19 19:31:33 CEST 2016

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