Q01532 (BLH1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Cysteine proteinase 1, mitochondrial
EC=3.4.22.40

Alternative name(s):
Bleomycin hydrolase
Short name=BLM hydrolase
Leucine aminopeptidase 3
Y3
Homocysteine-thiolactonase
Short name=Hcy-thiolactonase
Short name=HTLase

Gene names

Name:	LAP3
Synonyms:	BLH1, GAL6, YCP1
Ordered Locus Names:	YNL239W
ORF Names:	N1118

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	483 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	The normal physiological role of the enzyme is unknown, but it is not essential for the viability of yeast cells. Has aminopeptidase activity, shortening substrate peptides sequentially by 1 amino acid. Has bleomycin hydrolase activity, which can protect the cell from the toxic effects of bleomycin. Has homocysteine-thiolactonase activity, protecting the cell against homocysteine toxicity. Acts as a repressor in the GAL4 regulatory system, but this does not require either the peptidase or nucleic acid-binding activities. Ref.11 Ref.15
Catalytic activity	Inactivates bleomycin B2 (a cytotoxic glycometallopeptide) by hydrolysis of a carboxyamide bond of beta-aminoalanine, but also shows general aminopeptidase activity. The specificity varies somewhat with source, but amino acid arylamides of Met, Leu and Ala are preferred.
Enzyme regulation	Inhibited by E64, a specific inhibitor of cysteine proteases, N-ethylmaleimide, iodacetamide, and mercury and zinc ions. Ref.1 Ref.3
Subunit structure	Homohexamer. Binds to nucleic acids. Binds single-stranded DNA and RNA with higher affinity than double-stranded DNA. Ref.8
Subcellular location	Mitochondrion. Cytoplasm Ref.10 Ref.12 Ref.14.
Post-translational modification	The N-terminus of isoform Cytoplasmic is blocked.
Miscellaneous	Present with 521 molecules/cell in log phase SD medium. Ref.13
Sequence similarities	Belongs to the peptidase C1 family.
Biophysicochemical properties	Kinetic parameters: N-terminal acetylation of lysine-4-methyl-7-coumarylamide (Ac-Lys-AMC) reduces the catalytic efficiency 50-fold towards this substrate. KM=12.8 µM for arginine-4-methyl-7-coumarylamide Ref.1 Ref.3 Ref.9 KM=0.33 mM for glutamine-beta-naphtylamide KM=228 µM for lysine-4-methyl-7-coumarylamide Vmax=2.56 µmol/h/mg enzyme for arginine-4-methyl-7-coumarylamide Vmax=370 nmol/min/mg enzyme for glutamine-beta-naphtylamide pH dependence: Optimum pH is 7.5.
Mass spectrometry	Molecular mass is 51830 Da from positions 31 - 482. Determined by ESI. Ref.6

Ontologies

Keywords
Cellular component	Cytoplasm Mitochondrion
Coding sequence diversity	Alternative initiation
Domain	Transit peptide
Ligand	DNA-binding
Molecular function	Hydrolase Protease Thiol protease
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	homocysteine catabolic process Ref.15 Inferred from direct assay. Source: SGD proteolysis Inferred from electronic annotation. Source: InterPro response to antibiotic Ref.9 Inferred from direct assay. Source: SGD
Cellular component	mitochondrion Ref.12 Ref.14 Inferred from direct assay. Source: SGD
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro transcription regulator activity Ref.6 Inferred from direct assay. Source: SGD
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]

Isoform Mitochondrial (identifier: Q01532-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform Cytoplasmic (identifier: Q01532-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-29: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 30

30

Mitochondrion Potential

Chain

31 – 482

452

Cysteine proteinase 1, mitochondrial

PRO_0000050554

Propeptide

483

1

Removed in mature form; by autocatalysis

PRO_0000292865

Sites

Active site

102

1

Active site

398

1

Active site

421

1

Amino acid modifications

Modified residue

296

1

Phosphothreonine Ref.17

Modified residue

356

1

Phosphothreonine Ref.17

Natural variations

Alternative sequence

1 – 29

29

Missing in isoform Cytoplasmic.

VSP_026453

Experimental info

Mutagenesis

102

1

C → A: Abolishes peptidase activity, which also hinders autocatalytic processing of the enzyme to the mature form. Ref.6

Mutagenesis

271 – 274

4

KDKK → ADAA in GAL6DB; disrupts nucleic acid-binding activity, but retains normal peptidase activity. Ref.6

Mutagenesis

398

1

H → A: Abolishes Hcy-thiolactonase activity. Ref.15

Mutagenesis

479

1

G → A: Results in the abnormal cleavage of 3 C-terminal residues instead of only 1 during autocatalytic processing. Ref.18

Sequence conflict

187

1

I → M in CAA48878. Ref.2

Secondary structure

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483

Helix Strand Turn

Details...

Helix

36 – 47

12

Helix

50 – 59

10

Helix

64 – 68

5

Helix

71 – 77

7

Beta strand

83 – 85

3

Beta strand

98 – 100

3

Helix

102 – 118

17

Helix

128 – 149

22

Turn

150 – 152

3

Helix

158 – 165

8

Helix

174 – 184

11

Helix

189 – 191

3

Helix

197 – 200

4

Helix

203 – 226

24

Beta strand

229 – 231

3

Helix

232 – 252

21

Beta strand

264 – 269

6

Beta strand

275 – 280

6

Helix

282 – 288

7

Beta strand

296 – 301

6

Beta strand

311 – 314

4

Beta strand

326 – 330

5

Helix

333 – 345

13

Beta strand

350 – 354

5

Turn

356 – 359

4

Turn

362 – 365

4

Helix

374 – 377

4

Helix

385 – 390

6

Beta strand

398 – 407

10

Turn

409 – 411

3

Beta strand

413 – 420

8

Beta strand

432 – 436

5

Helix

437 – 443

7

Beta strand

444 – 450

7

Helix

451 – 453

3

Helix

456 – 463

8

Beta strand

470 – 472

3

Helix

477 – 479

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform Mitochondrial [UniParc]. Last modified June 26, 2007. Version 3. Checksum: BF92A6049F98DD3D	FASTA	483	55,483
	10 20 30 40 50 60 MLPTSVSRSL YLKTFRSHLL RAPQIVLKRM SSSIDISKIN SWNKEFQSDL THQLATTVLK 70 80 90 100 110 120 NYNADDALLN KTRLQKQDNR VFNTVVSTDS TPVTNQKSSG RCWLFAATNQ LRLNVLSELN 130 140 150 160 170 180 LKEFELSQAY LFFYDKLEKA NYFLDQIVSS ADQDIDSRLV QYLLAAPTED GGQYSMFLNL 190 200 210 220 230 240 VKKYGLIPKD LYGDLPYSTT ASRKWNSLLT TKLREFAETL RTALKERSAD DSIIVTLREQ 250 260 270 280 290 300 MQREIFRLMS LFMDIPPVQP NEQFTWEYVD KDKKIHTIKS TPLEFASKYA KLDPSTPVSL 310 320 330 340 350 360 INDPRHPYGK LIKIDRLGNV LGGDAVIYLN VDNETLSKLV VKRLQNNKAV FFGSHTPKFM 370 380 390 400 410 420 DKKTGVMDIE LWNYPAIGYN LPQQKASRIR YHESLMTHAM LITGCHVDET SKLPLRYRVE 430 440 450 460 470 480 NSWGKDSGKD GLYVMTQKYF EEYCFQIVVD INELPKELAS KFTSGKEEPI VLPIWDPMGA LAK
	Isoform Cytoplasmic. Checksum: 2F4B6236AEE3BABF	FASTA	454	52,089
	10 20 30 40 50 60 MSSSIDISKI NSWNKEFQSD LTHQLATTVL KNYNADDALL NKTRLQKQDN RVFNTVVSTD 70 80 90 100 110 120 STPVTNQKSS GRCWLFAATN QLRLNVLSEL NLKEFELSQA YLFFYDKLEK ANYFLDQIVS 130 140 150 160 170 180 SADQDIDSRL VQYLLAAPTE DGGQYSMFLN LVKKYGLIPK DLYGDLPYST TASRKWNSLL 190 200 210 220 230 240 TTKLREFAET LRTALKERSA DDSIIVTLRE QMQREIFRLM SLFMDIPPVQ PNEQFTWEYV 250 260 270 280 290 300 DKDKKIHTIK STPLEFASKY AKLDPSTPVS LINDPRHPYG KLIKIDRLGN VLGGDAVIYL 310 320 330 340 350 360 NVDNETLSKL VVKRLQNNKA VFFGSHTPKF MDKKTGVMDI ELWNYPAIGY NLPQQKASRI 370 380 390 400 410 420 RYHESLMTHA MLITGCHVDE TSKLPLRYRV ENSWGKDSGK DGLYVMTQKY FEEYCFQIVV 430 440 450 DINELPKELA SKFTSGKEEP IVLPIWDPMG ALAK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and characterization of a cysteine proteinase from Saccharomyces cerevisiae." Kambouris N.G., Burke D.J., Creutz C.E. J. Biol. Chem. 267:21570-21576(1992) [PubMed: 1400467] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
[2]	"A yeast gene (BLH1) encodes a polypeptide with high homology to vertebrate bleomycin hydrolase, a family member of thiol proteinases." Magdolen U., Mueller G., Magdolen V., Bandlow W. Biochim. Biophys. Acta 1171:299-303(1993) [PubMed: 8424954] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 228-250 AND 367-387.
[3]	"BLH1 codes for a yeast thiol aminopeptidase, the equivalent of mammalian bleomycin hydrolase." Enenkel C., Wolf D.H. J. Biol. Chem. 268:7036-7043(1993) [PubMed: 8463237] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
[4]	"The DNA sequence of cosmid 14-5 from chromosome XIV reveals 21 open reading frames including a novel gene encoding a globin-like domain." Pandolfo D., de Antoni A., Lanfranchi G., Valle G. Yeast 12:1071-1076(1996) [PubMed: 8896273] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[5]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications." Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J. Nature 387:93-98(1997) [PubMed: 9169873] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[6]	"The cysteine-peptidase bleomycin hydrolase is a member of the galactose regulon in yeast." Zheng W., Xu H.E., Johnston S.A. J. Biol. Chem. 272:30350-30355(1997) [PubMed: 9374524] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-58, MASS SPECTROMETRY, MUTAGENESIS OF CYS-102 AND 271-LYS--LYS-274.
[7]	"Calcium-dependent secretory vesicle-binding and lipid-binding proteins of Saccharomyces cerevisiae." Creutz C.E., Snyder S.L., Kambouris N.G. Yeast 7:229-244(1991) [PubMed: 1882548] [Abstract] Cited for: PROTEIN SEQUENCE OF 228-251 AND 367-387.
[8]	"Crystal structure of a conserved protease that binds DNA: the bleomycin hydrolase, Gal6." Joshua-Tor L., Xu H.E., Johnston S.A., Rees D.C. Science 269:945-950(1995) [PubMed: 7638617] [Abstract] Cited for: PROTEIN SEQUENCE OF C-TERMINUS, X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 30-483, SUBUNIT.
[9]	"Yeast bleomycin hydrolase is a DNA-binding cysteine protease. Identification, purification, biochemical characterization." Xu H.E., Johnston S.A. J. Biol. Chem. 269:21177-21183(1994) [PubMed: 8063738] [Abstract] Cited for: DNA-BINDING, BIOPHYSICOCHEMICAL PROPERTIES.
[10]	"The nucleic acid binding activity of bleomycin hydrolase is involved in bleomycin detoxification." Zheng W., Johnston S.A. Mol. Cell. Biol. 18:3580-3585(1998) [PubMed: 9584198] [Abstract] Cited for: DNA-BINDING, SUBCELLULAR LOCATION.
[11]	"Cellular resistance to bleomycin in Saccharomyces cerevisiae is not affected by changes in bleomycin hydrolase levels." Wang H., Ramotar D. Biochem. Cell Biol. 80:789-796(2002) [PubMed: 12555812] [Abstract] Cited for: FUNCTION.
[12]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed: 14562095] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[13]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[14]	"The proteome of Saccharomyces cerevisiae mitochondria." Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R.P., Meyer H.E., Schoenfisch B., Perschil I., Chacinska A., Guiard B., Rehling P., Pfanner N., Meisinger C. Proc. Natl. Acad. Sci. U.S.A. 100:13207-13212(2003) [PubMed: 14576278] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY. Strain: ATCC 76625 / YPH499.
[15]	"Protective mechanisms against homocysteine toxicity: the role of bleomycin hydrolase." Zimny J., Sikora M., Guranowski A., Jakubowski H. J. Biol. Chem. 281:22485-22492(2006) [PubMed: 16769724] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF HIS-398.
[16]	"A large-scale full-length cDNA analysis to explore the budding yeast transcriptome." Miura F., Kawaguchi N., Sese J., Toyoda A., Hattori M., Morishita S., Ito T. Proc. Natl. Acad. Sci. U.S.A. 103:17846-17851(2006) [PubMed: 17101987] [Abstract] Cited for: ALTERNATIVE INITIATION.
[17]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-296 AND THR-356, MASS SPECTROMETRY.
[18]	"The unusual active site of Gal6/bleomycin hydrolase can act as a carboxypeptidase, aminopeptidase, and peptide ligase." Zheng W., Johnston S.A., Joshua-Tor L. Cell 93:103-109(1998) [PubMed: 9546396] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) OF 30-483 OF MUTANT ALA-102, MUTAGENESIS OF GLY-479.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M97910 Genomic DNA. Translation: AAA35231.1.
X69124 Genomic DNA. Translation: CAA48878.1.
X68228 Genomic DNA. Translation: CAA48309.1.
Z71515 Genomic DNA. Translation: CAA96144.1.
Z69381 Genomic DNA. Translation: CAA93359.1.
U74299 Genomic DNA. Translation: AAB18260.1.

PIR

S25606. A46093.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A6R	X-ray	2.05	A	32-483	[»]
1GCB	X-ray	2.20	A	30-483	[»]
2DZY	X-ray	2.57	A	30-482	[»]
2DZZ	X-ray	2.15	A	30-482	[»]
2E00	X-ray	2.00	A	30-482	[»]
2E01	X-ray	1.73	A	30-482	[»]
2E02	X-ray	2.20	A	30-482	[»]
2E03	X-ray	2.13	A	30-482	[»]
3GCB	X-ray	1.87	A	32-482	[»]

ProteinModelPortal

Q01532.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2941N.

IntAct

Q01532. 12 interactions.

MINT

MINT-513897.

STRING

Q01532.

Protein family/group databases

MEROPS

C01.085.

Proteomic databases

PeptideAtlas

Q01532.

PRIDE

Q01532.

Genome annotation databases

EnsemblFungi

YNL239W; YNL239W; YNL239W.

GenomeReviews

Gene locus YNL239W in contig Y13139_GR.

KEGG

sce:YNL239W.

NMPDR

fig|4932.3.peg.5225.

Organism-specific databases

CYGD

YNL239w.

SGD

S000005183. LAP3.

Phylogenomic databases

eggNOG

fuNOG04832.

HOGENOM

HBG350935.

OMA

KLYTVDY.

OrthoDB

EOG96DNKS.

Enzyme and pathway databases

BRENDA

3.4.22.40. 250.

Gene expression databases

ArrayExpress

Q01532.

Genevestigator

Q01532.

GermOnline

YNL239W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000169. Pept_cys_AS.
IPR004134. Peptidase_C1B.
[Graphical view]

PANTHER

PTHR10363. Peptidase_C1B. 1 hit.

Pfam

PF03051. Peptidase_C1_2. 1 hit.
[Graphical view]

PIRSF

PIRSF005700. PepC. 1 hit.

PROSITE

PS00640. THIOL_PROTEASE_ASN. False negative.
PS00139. THIOL_PROTEASE_CYS. 1 hit.
PS00639. THIOL_PROTEASE_HIS. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

979451.

Entry information

Entry name

BLH1_YEAST

Accession

Primary (citable) accession number: Q01532

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	June 26, 2007
Last modified:	August 10, 2010
This is version 111 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)