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
Homocysteine-thiolactonase
Short name=HTLase
Short name=Hcy-thiolactonase
Leucine aminopeptidase 3
Y3

Gene names

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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

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.12 Ref.16
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.9
Subcellular location	Isoform Cytoplasmic: Cytoplasm Ref.11 Ref.13 Ref.15. Isoform Mitochondrial: Mitochondrion Ref.11 Ref.13 Ref.15.
Post-translational modification	The N-terminus of isoform Cytoplasmic is blocked.
Miscellaneous	Present with 521 molecules/cell in log phase SD medium.
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.10 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.7

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 Reference proteome
Gene Ontology (GO)
Biological_process	homocysteine catabolic process Inferred from mutant phenotype Ref.16. Source: SGD negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.7. Source: SGD proteolysis Inferred from electronic annotation. Source: UniProtKB-KW response to antibiotic Inferred from direct assay Ref.10. Source: SGD
Cellular_component	mitochondrion Inferred from direct assay Ref.13Ref.15PubMed 16823961. Source: SGD
Molecular_function	RNA polymerase II core promoter proximal region sequence-specific DNA binding Inferred from direct assay Ref.10. Source: SGD cysteine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro cysteine-type peptidase activity Inferred from direct assay Ref.10. Source: SGD double-stranded DNA binding Inferred from direct assay Ref.11. Source: SGD mRNA binding Inferred from direct assay PubMed 21124907. Source: SGD single-stranded DNA binding Inferred from direct assay Ref.11. 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.

Note: Produced by alternative initiation at Met-30 of isoform Mitochondrial.

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.18

Modified residue

356

1

Phosphothreonine Ref.18

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.7

Mutagenesis

271 – 274

4

KDKK → ADAA in GAL6DB; disrupts nucleic acid-binding activity, but retains normal peptidase activity. Ref.7

Mutagenesis

398

1

H → A: Abolishes Hcy-thiolactonase activity. Ref.16

Mutagenesis

479

1

G → A: Results in the abnormal cleavage of 3 C-terminal residues instead of only 1 during autocatalytic processing. Ref.19

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

414 – 420

7

Turn

425 – 428

4

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 [UniParc]. 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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[6]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[7]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-58, MASS SPECTROMETRY, MUTAGENESIS OF CYS-102 AND 271-LYS--LYS-274.
[8]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 228-251 AND 367-387.
[9]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF C-TERMINUS, X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 30-483, SUBUNIT.
[10]	"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] [Europe PMC] [Abstract] Cited for: DNA-BINDING, BIOPHYSICOCHEMICAL PROPERTIES.
[11]	"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] [Europe PMC] [Abstract] Cited for: DNA-BINDING, SUBCELLULAR LOCATION.
[12]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION.
[13]	"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] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[14]	"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] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[15]	"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] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY. Strain: ATCC 76625 / YPH499.
[16]	"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] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF HIS-398.
[17]	"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] [Europe PMC] [Abstract] Cited for: ALTERNATIVE INITIATION.
[18]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-296 AND THR-356, MASS SPECTROMETRY.
[19]	"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] [Europe PMC] [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.
BK006947 Genomic DNA. Translation: DAA10320.1.

PIR

S25606. A46093.

RefSeq

NP_014160.2. NM_001183077.1.

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.

SMR

Q01532. Positions 30-482.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2941N.

IntAct

Q01532. 11 interactions.

MINT

MINT-513897.

STRING

4932.YNL239W.

Protein family/group databases

MEROPS

C01.085.

Proteomic databases

PaxDb

Q01532.

PeptideAtlas

Q01532.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

855482.

KEGG

sce:YNL239W.

Organism-specific databases

CYGD

YNL239w.

SGD

S000005183. LAP3.

Phylogenomic databases

eggNOG

COG3579.

HOGENOM

HOG000064089.

KO

K01372.

OMA

GCDVGQE.

OrthoDB

EOG4MGWH0.

Enzyme and pathway databases

BRENDA

3.4.22.40. 984.

SABIO-RK

Q01532.

Gene expression databases

Genevestigator

Q01532.

GermOnline

YNL239W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR000169. Pept_cys_AS.
IPR025660. Pept_his_AS.
IPR004134. Peptidase_C1B.
[Graphical view]

PANTHER

PTHR10363. PTHR10363. 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

EvolutionaryTrace

Q01532.

NextBio

979451.

Entry information

Entry name

BLH1_YEAST

Accession

Primary (citable) accession number: Q01532
Secondary accession number(s): D6W0V4

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	June 26, 2007
Last modified:	May 1, 2013
This is version 135 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program