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Granzyme A (EC 3.4.21.78) (CTL tryptase) (Cytotoxic T-lymphocyte proteinase 1) (Fragmentin-1) (Granzyme-1) (Hanukkah factor) (H factor) (HF)

 GRAA_HUMAN              Reviewed;         262 AA.
P12544; A4PHN1; Q6IB36;
01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
11-JAN-2011, sequence version 2.
07-JUN-2017, entry version 186.
RecName: Full=Granzyme A;
EC=3.4.21.78;
AltName: Full=CTL tryptase;
AltName: Full=Cytotoxic T-lymphocyte proteinase 1;
AltName: Full=Fragmentin-1;
AltName: Full=Granzyme-1;
AltName: Full=Hanukkah factor;
Short=H factor;
Short=HF;
Flags: Precursor;
Name=GZMA; Synonyms=CTLA3, HFSP;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM ALPHA), AND VARIANT THR-121.
TISSUE=T-cell;
PubMed=3257574; DOI=10.1073/pnas.85.4.1184;
Gershenfeld H.K., Hershberger R.J., Shows T.B., Weissman I.L.;
"Cloning and chromosomal assignment of a human cDNA encoding a T
cell- and natural killer cell-specific trypsin-like serine protease.";
Proc. Natl. Acad. Sci. U.S.A. 85:1184-1188(1988).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM ALPHA), AND VARIANT
THR-121.
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.;
"Cloning of human full open reading frames in Gateway(TM) system entry
vector (pDONR201).";
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15372022; DOI=10.1038/nature02919;
Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S.,
Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M.,
She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.,
Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M.,
Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T.,
Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M.,
Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K.,
Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C.,
Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M.,
Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A.,
Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M.,
Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M.,
Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S.,
Richardson P., Lucas S.M., Myers R.M., Rubin E.M.;
"The DNA sequence and comparative analysis of human chromosome 5.";
Nature 431:268-274(2004).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM ALPHA), AND VARIANT
THR-121.
TISSUE=Blood;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-72, NUCLEOTIDE SEQUENCE [MRNA]
OF 1-34 (ISOFORM BETA), ALTERNATIVE PROMOTER USAGE, AND INDUCTION.
PubMed=17180578; DOI=10.1007/s10038-006-0099-9;
Ruike Y., Katsuma S., Hirasawa A., Tsujimoto G.;
"Glucocorticoid-induced alternative promoter usage for a novel 5'
variant of granzyme A.";
J. Hum. Genet. 52:172-178(2007).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-23.
Goralski T.J., Krensky A.M.;
"The upstream region of the human granzyme A locus contains both
positive and negative transcriptional regulatory elements.";
Submitted (NOV-1995) to the EMBL/GenBank/DDBJ databases.
[7]
PROTEIN SEQUENCE OF 29-53.
PubMed=3047119;
Poe M., Bennett C.D., Biddison W.E., Blake J.T., Norton G.P.,
Rodkey J.A., Sigal N.H., Turner R.V., Wu J.K., Zweerink H.J.;
"Human cytotoxic lymphocyte tryptase. Its purification from granules
and the characterization of inhibitor and substrate specificity.";
J. Biol. Chem. 263:13215-13222(1988).
[8]
PROTEIN SEQUENCE OF 29-40, AND CHARACTERIZATION.
PubMed=3262682;
Hameed A., Lowrey D.M., Lichtenheld M., Podack E.R.;
"Characterization of three serine esterases isolated from human IL-2
activated killer cells.";
J. Immunol. 141:3142-3147(1988).
[9]
PROTEIN SEQUENCE OF 29-39, AND CHARACTERIZATION.
PubMed=3263427;
Kraehenbuhl O., Rey C., Jenne D.E., Lanzavecchia A., Groscurth P.,
Carrel S., Tschopp J.;
"Characterization of granzymes A and B isolated from granules of
cloned human cytotoxic T lymphocytes.";
J. Immunol. 141:3471-3477(1988).
[10]
FUNCTION AS SET PROTEASE.
PubMed=11555662; DOI=10.1074/jbc.M108137200;
Beresford P.J., Zhang D., Oh D.Y., Fan Z., Greer E.L., Russo M.L.,
Jaju M., Lieberman J.;
"Granzyme A activates an endoplasmic reticulum-associated caspase-
independent nuclease to induce single-stranded DNA nicks.";
J. Biol. Chem. 276:43285-43293(2001).
[11]
FUNCTION AS SET PROTEASE.
PubMed=12628186; DOI=10.1016/S0092-8674(03)00150-8;
Fan Z., Beresford P.J., Oh D.Y., Zhang D., Lieberman J.;
"Tumor suppressor NM23-H1 is a granzyme A-activated DNase during CTL-
mediated apoptosis, and the nucleosome assembly protein SET is its
inhibitor.";
Cell 112:659-672(2003).
[12]
FUNCTION, AND INTERACTION WITH APEX1.
PubMed=12524539; DOI=10.1038/ni885;
Fan Z., Beresford P.J., Zhang D., Xu Z., Novina C.D., Yoshida A.,
Pommier Y., Lieberman J.;
"Cleaving the oxidative repair protein Ape1 enhances cell death
mediated by granzyme A.";
Nat. Immunol. 4:145-153(2003).
[13]
FUNCTION AS SET PROTEASE.
PubMed=16818237; DOI=10.1016/j.molcel.2006.06.005;
Chowdhury D., Beresford P.J., Zhu P., Zhang D., Sung J.S., Demple B.,
Perrino F.W., Lieberman J.;
"The exonuclease TREX1 is in the SET complex and acts in concert with
NM23-H1 to degrade DNA during granzyme A-mediated cell death.";
Mol. Cell 23:133-142(2006).
[14]
GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-170.
TISSUE=Liver;
PubMed=19159218; DOI=10.1021/pr8008012;
Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.;
"Glycoproteomics analysis of human liver tissue by combination of
multiple enzyme digestion and hydrazide chemistry.";
J. Proteome Res. 8:651-661(2009).
[15]
3D-STRUCTURE MODELING OF 29-262.
PubMed=3237717; DOI=10.1002/prot.340040306;
Murphy M.E.P., Moult J., Bleackley R.C., Gershenfeld H.,
Weissman I.L., James M.N.G.;
"Comparative molecular model building of two serine proteinases from
cytotoxic T lymphocytes.";
Proteins 4:190-204(1988).
[16]
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 29-262 IN COMPLEX WITH A
TRIPEPTIDE CMK INHIBITOR.
PubMed=12819769; DOI=10.1038/nsb944;
Bell J.K., Goetz D.H., Mahrus S., Harris J.L., Fletterick R.J.,
Craik C.S.;
"The oligomeric structure of human granzyme A is a determinant of its
extended substrate specificity.";
Nat. Struct. Biol. 10:527-534(2003).
[17]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 29-262 IN COMPLEX WITH
SUBSTRATE.
PubMed=12819770; DOI=10.1038/nsb945;
Hink-Schauer C., Estebanez-Perpina E., Kurschus F.C., Bode W.,
Jenne D.E.;
"Crystal structure of the apoptosis-inducing human granzyme A dimer.";
Nat. Struct. Biol. 10:535-540(2003).
-!- FUNCTION: Abundant protease in the cytosolic granules of cytotoxic
T-cells and NK-cells which activates caspase-independent cell
death with morphological features of apoptosis when delivered into
the target cell through the immunological synapse. It cleaves
after Lys or Arg. Cleaves APEX1 after 'Lys-31' and destroys its
oxidative repair activity. Cleaves the nucleosome assembly protein
SET after 'Lys-189', which disrupts its nucleosome assembly
activity and allows the SET complex to translocate into the
nucleus to nick and degrade the DNA. {ECO:0000269|PubMed:11555662,
ECO:0000269|PubMed:12524539, ECO:0000269|PubMed:12628186,
ECO:0000269|PubMed:16818237}.
-!- CATALYTIC ACTIVITY: Hydrolysis of proteins, including fibronectin,
type IV collagen and nucleolin. Preferential cleavage: -Arg-|-
Xaa-, -Lys-|-Xaa- >> -Phe-|-Xaa- in small molecule substrates.
-!- SUBUNIT: Homodimer; disulfide-linked. Interacts with APEX1.
{ECO:0000269|PubMed:12524539, ECO:0000269|PubMed:12819769,
ECO:0000269|PubMed:12819770}.
-!- SUBCELLULAR LOCATION: Isoform alpha: Secreted. Cytoplasmic
granule.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative promoter usage; Named isoforms=2;
Name=alpha;
IsoId=P12544-1; Sequence=Displayed;
Name=beta;
IsoId=P12544-2; Sequence=VSP_038571, VSP_038572;
-!- INDUCTION: Dexamethasone (DEX) induces expression of isoform beta
and represses expression of isoform alpha. The alteration in
expression is mediated by binding of glucocorticoid receptor to
independent promoters adjacent to the alternative first exons of
isoform alpha and isoform beta. {ECO:0000269|PubMed:17180578}.
-!- SIMILARITY: Belongs to the peptidase S1 family. Granzyme
subfamily. {ECO:0000255|PROSITE-ProRule:PRU00274}.
-!- CAUTION: Exons 1a and 1b of the sequence reported in
PubMed:17180578 are of human origin, however exon 2 shows strong
similarity to the rat sequence. {ECO:0000305}.
-!- WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology
and Haematology;
URL="http://atlasgeneticsoncology.org/Genes/GZMAID51130ch5q11.html";
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EMBL; M18737; AAA52647.1; -; mRNA.
EMBL; CR456968; CAG33249.1; -; mRNA.
EMBL; AC091977; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC015739; AAH15739.1; -; mRNA.
EMBL; AB284134; BAF56159.1; -; mRNA.
EMBL; U40006; AAD00009.1; -; Genomic_DNA.
CCDS; CCDS3965.1; -. [P12544-1]
PIR; A31372; A31372.
RefSeq; NP_006135.1; NM_006144.3.
UniGene; Hs.90708; -.
PDB; 1HF1; Model; -; A=29-262.
PDB; 1OP8; X-ray; 2.50 A; A/B/C/D/E/F=29-262.
PDB; 1ORF; X-ray; 2.40 A; A=29-262.
PDBsum; 1HF1; -.
PDBsum; 1OP8; -.
PDBsum; 1ORF; -.
ProteinModelPortal; P12544; -.
SMR; P12544; -.
BioGrid; 109256; 17.
IntAct; P12544; 4.
STRING; 9606.ENSP00000274306; -.
ChEMBL; CHEMBL4307; -.
MEROPS; S01.135; -.
iPTMnet; P12544; -.
PhosphoSitePlus; P12544; -.
BioMuta; GZMA; -.
DMDM; 317373360; -.
MaxQB; P12544; -.
PaxDb; P12544; -.
PeptideAtlas; P12544; -.
PRIDE; P12544; -.
DNASU; 3001; -.
Ensembl; ENST00000274306; ENSP00000274306; ENSG00000145649. [P12544-1]
GeneID; 3001; -.
KEGG; hsa:3001; -.
UCSC; uc003jpm.4; human. [P12544-1]
CTD; 3001; -.
DisGeNET; 3001; -.
GeneCards; GZMA; -.
HGNC; HGNC:4708; GZMA.
HPA; HPA054134; -.
MIM; 140050; gene.
neXtProt; NX_P12544; -.
OpenTargets; ENSG00000145649; -.
PharmGKB; PA29086; -.
eggNOG; KOG3627; Eukaryota.
eggNOG; COG5640; LUCA.
GeneTree; ENSGT00760000118895; -.
HOGENOM; HOG000251820; -.
HOVERGEN; HBG013304; -.
InParanoid; P12544; -.
KO; K01352; -.
OMA; KEFPYPC; -.
OrthoDB; EOG091G0AH5; -.
PhylomeDB; P12544; -.
TreeFam; TF333630; -.
BRENDA; 3.4.21.78; 2681.
SIGNOR; P12544; -.
EvolutionaryTrace; P12544; -.
GeneWiki; GZMA; -.
GenomeRNAi; 3001; -.
PRO; PR:P12544; -.
Proteomes; UP000005640; Chromosome 5.
Bgee; ENSG00000145649; -.
CleanEx; HS_GZMA; -.
Genevisible; P12544; HS.
GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
GO; GO:0001772; C:immunological synapse; TAS:UniProtKB.
GO; GO:0005634; C:nucleus; TAS:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
GO; GO:0004252; F:serine-type endopeptidase activity; IDA:UniProtKB.
GO; GO:0006915; P:apoptotic process; TAS:UniProtKB.
GO; GO:0019835; P:cytolysis; IEA:UniProtKB-KW.
GO; GO:0006955; P:immune response; TAS:UniProtKB.
GO; GO:0043392; P:negative regulation of DNA binding; IDA:UniProtKB.
GO; GO:0032078; P:negative regulation of endodeoxyribonuclease activity; IDA:UniProtKB.
GO; GO:0051354; P:negative regulation of oxidoreductase activity; IDA:UniProtKB.
GO; GO:0043065; P:positive regulation of apoptotic process; IDA:UniProtKB.
GO; GO:0051603; P:proteolysis involved in cellular protein catabolic process; IDA:UniProtKB.
CDD; cd00190; Tryp_SPc; 1.
InterPro; IPR009003; Peptidase_S1_PA.
InterPro; IPR001314; Peptidase_S1A.
InterPro; IPR001254; Trypsin_dom.
InterPro; IPR018114; TRYPSIN_HIS.
InterPro; IPR033116; TRYPSIN_SER.
Pfam; PF00089; Trypsin; 1.
PRINTS; PR00722; CHYMOTRYPSIN.
SMART; SM00020; Tryp_SPc; 1.
SUPFAM; SSF50494; SSF50494; 1.
PROSITE; PS50240; TRYPSIN_DOM; 1.
PROSITE; PS00134; TRYPSIN_HIS; 1.
PROSITE; PS00135; TRYPSIN_SER; 1.
1: Evidence at protein level;
3D-structure; Alternative promoter usage; Apoptosis;
Complete proteome; Cytolysis; Direct protein sequencing;
Disulfide bond; Glycoprotein; Hydrolase; Polymorphism; Protease;
Reference proteome; Secreted; Serine protease; Signal; Zymogen.
SIGNAL 1 26 In isoform alpha.
PROPEP 27 28 Activation peptide (in isoform alpha).
{ECO:0000269|PubMed:3047119,
ECO:0000269|PubMed:3262682,
ECO:0000269|PubMed:3263427}.
/FTId=PRO_0000027393.
CHAIN 29 262 Granzyme A.
/FTId=PRO_0000027394.
DOMAIN 29 259 Peptidase S1. {ECO:0000255|PROSITE-
ProRule:PRU00274}.
ACT_SITE 69 69 Charge relay system.
ACT_SITE 114 114 Charge relay system.
ACT_SITE 212 212 Charge relay system.
CARBOHYD 170 170 N-linked (GlcNAc...) asparagine.
{ECO:0000269|PubMed:19159218}.
DISULFID 54 70
DISULFID 148 218
DISULFID 179 197
DISULFID 208 234
VAR_SEQ 1 17 Missing (in isoform beta).
{ECO:0000303|PubMed:17180578}.
/FTId=VSP_038571.
VAR_SEQ 18 23 LLLIPE -> MTKGLR (in isoform beta).
{ECO:0000303|PubMed:17180578}.
/FTId=VSP_038572.
VARIANT 121 121 M -> T (in dbSNP:rs3104233).
{ECO:0000269|PubMed:15489334,
ECO:0000269|PubMed:3257574,
ECO:0000269|Ref.2}.
/FTId=VAR_024291.
CONFLICT 33 34 NE -> DT (in Ref. 5; no nucleotide
entry). {ECO:0000305}.
CONFLICT 36 36 T -> V (in Ref. 5; no nucleotide entry).
{ECO:0000305}.
CONFLICT 47 47 S -> K (in Ref. 5; no nucleotide entry).
{ECO:0000305}.
CONFLICT 49 52 DRKT -> KPDS (in Ref. 5; no nucleotide
entry). {ECO:0000305}.
CONFLICT 62 62 D -> N (in Ref. 5; no nucleotide entry).
{ECO:0000305}.
CONFLICT 71 72 NL -> IP (in Ref. 5; no nucleotide
entry). {ECO:0000305}.
STRAND 43 47 {ECO:0000244|PDB:1ORF}.
STRAND 49 51 {ECO:0000244|PDB:1ORF}.
STRAND 53 60 {ECO:0000244|PDB:1ORF}.
STRAND 63 66 {ECO:0000244|PDB:1ORF}.
STRAND 77 81 {ECO:0000244|PDB:1ORF}.
STRAND 83 87 {ECO:0000244|PDB:1ORF}.
STRAND 93 95 {ECO:0000244|PDB:1ORF}.
STRAND 97 102 {ECO:0000244|PDB:1ORF}.
TURN 108 110 {ECO:0000244|PDB:1ORF}.
STRAND 116 122 {ECO:0000244|PDB:1ORF}.
STRAND 127 130 {ECO:0000244|PDB:1ORF}.
STRAND 147 154 {ECO:0000244|PDB:1ORF}.
STRAND 156 160 {ECO:0000244|PDB:1ORF}.
STRAND 167 174 {ECO:0000244|PDB:1ORF}.
HELIX 176 179 {ECO:0000244|PDB:1ORF}.
TURN 182 189 {ECO:0000244|PDB:1ORF}.
STRAND 195 199 {ECO:0000244|PDB:1ORF}.
STRAND 215 218 {ECO:0000244|PDB:1ORF}.
STRAND 221 228 {ECO:0000244|PDB:1ORF}.
STRAND 241 245 {ECO:0000244|PDB:1ORF}.
HELIX 248 258 {ECO:0000244|PDB:1ORF}.
SEQUENCE 262 AA; 28999 MW; FD773628BA6F301B CRC64;
MRNSYRFLAS SLSVVVSLLL IPEDVCEKII GGNEVTPHSR PYMVLLSLDR KTICAGALIA
KDWVLTAAHC NLNKRSQVIL GAHSITREEP TKQIMLVKKE FPYPCYDPAT REGDLKLLQL
MEKAKINKYV TILHLPKKGD DVKPGTMCQV AGWGRTHNSA SWSDTLREVN ITIIDRKVCN
DRNHYNFNPV IGMNMVCAGS LRGGRDSCNG DSGSPLLCEG VFRGVTSFGL ENKCGDPRGP
GVYILLSKKH LNWIIMTIKG AV


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