Reviewed, UniProtKB/Swiss-Prot P10507 (MPPB_YEAST)

Names and origin

Protein names

Recommended name:
    Mitochondrial-processing peptidase subunit beta
    EC=3.4.24.64
Alternative name(s):
    Beta-MPP
    PEP

Gene names

Name:	MAS1
Synonyms:	MIF1
Ordered Locus Names:	YLR163C
ORF Names:	L9632.10

Organism

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

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	462 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	Cleaves presequences (transit peptides) from mitochondrial protein precursors.
Catalytic activity	Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.
Cofactor	Binds 1 zinc ion per subunit.
Subunit structure	Heterodimer of alpha and beta subunits.
Subcellular location	Mitochondrion matrix.
Miscellaneous	Present with 1360 molecules/cell in log phase SD medium. Ref.5
Sequence similarities	Belongs to the peptidase M16 family.

Ontologies

Keywords
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	Metal-binding Zinc
Molecular function	Hydrolase Metalloprotease Protease
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	mitochondrial protein processing during import Ref.4 Inferred from direct assay. Source: SGD proteolysis Inferred from electronic annotation. Source: InterPro
Cellular component	mitochondrial processing peptidase complex Inferred from direct assay. Source: SGD
Molecular function	metalloendopeptidase activity Inferred from electronic annotation. Source: InterPro protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
MSH1	P25846	1	EBI-11212,EBI-11347
TAF2	P23255	1	EBI-11212,EBI-18862

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Transit peptide

1 – 20

20

Mitochondrion Ref.4

Chain

21 – 462

442

Mitochondrial-processing peptidase subunit beta

PRO_0000026784

Sites

Active site

73

1

Proton acceptor

Metal binding

70

1

Zinc

Metal binding

74

1

Zinc

Metal binding

150

1

Zinc

Amino acid modifications

Modified residue

243

1

Phosphoserine Ref.6

Experimental info

Mutagenesis

73

1

E → Q: Loss of activity. Ref.7

Secondary structure

1

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462

Helix Strand Turn

Details...

Beta strand

27 – 30

4

Beta strand

36 – 41

6

Beta strand

46 – 55

10

Helix

58 – 60

3

Turn

63 – 67

5

Helix

68 – 75

8

Beta strand

78 – 82

5

Helix

85 – 94

10

Beta strand

98 – 103

6

Beta strand

105 – 115

11

Helix

116 – 118

3

Helix

119 – 131

13

Helix

137 – 154

18

Helix

158 – 170

13

Turn

171 – 173

3

Helix

175 – 177

3

Helix

184 – 189

6

Helix

192 – 202

11

Helix

205 – 207

3

Beta strand

208 – 215

8

Helix

218 – 229

12

Beta strand

254 – 259

6

Beta strand

264 – 273

10

Helix

282 – 292

11

Beta strand

294 – 296

3

Turn

297 – 299

3

Beta strand

302 – 305

4

Helix

308 – 314

7

Beta strand

321 – 329

9

Beta strand

334 – 343

10

Turn

344 – 346

3

Helix

349 – 364

16

Helix

370 – 385

16

Helix

391 – 405

15

Helix

411 – 419

9

Helix

423 – 433

11

Beta strand

434 – 436

3

Beta strand

439 – 445

7

Helix

447 – 449

3

Helix

453 – 461

9

Sequences

	Sequence		Length	Mass (Da)
	P10507-1 [UniParc]. Last modified July 1, 1989. Version 1. Checksum: 084CE63C495EDFC4	FASTA	462	51,084
	10 20 30 40 50 60 MFSRTASKFR NTRRLLSTIS SQIPGTRTSK LPNGLTIATE YIPNTSSATV GIFVDAGSRA 70 80 90 100 110 120 ENVKNNGTAH FLEHLAFKGT QNRSQQGIEL EIENIGSHLN AYTSRENTVY YAKSLQEDIP 130 140 150 160 170 180 KAVDILSDIL TKSVLDNSAI ERERDVIIRE SEEVDKMYDE VVFDHLHEIT YKDQPLGRTI 190 200 210 220 230 240 LGPIKNIKSI TRTDLKDYIT KNYKGDRMVL AGAGAVDHEK LVQYAQKYFG HVPKSESPVP 250 260 270 280 290 300 LGSPRGPLPV FCRGERFIKE NTLPTTHIAI ALEGVSWSAP DYFVALATQA IVGNWDRAIG 310 320 330 340 350 360 TGTNSPSPLA VAASQNGSLA NSYMSFSTSY ADSGLWGMYI VTDSNEHNVQ LIVNEILKEW 370 380 390 400 410 420 KRIKSGKISD AEVNRAKAQL KAALLLSLDG STAIVEDIGR QVVTTGKRLS PEEVFEQVDK 430 440 450 460 ITKDDIIMWA NYRLQNKPVS MVALGNTSTV PNVSYIEEKL NQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"MAS1, a gene essential for yeast mitochondrial assembly, encodes a subunit of the mitochondrial processing protease." Witte C., Jensen R.E., Yaffe M.P., Schatz G. EMBO J. 7:1439-1447(1988) [PubMed: 3044780] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XII." Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H. , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D. Nature 387:87-90(1997) [PubMed: 9169871] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"The MAS-encoded processing protease of yeast mitochondria. Interaction of the purified enzyme with signal peptides and a purified precursor protein." Yang M., Geli V., Oppliger W., Suda K., James P., Schatz G. J. Biol. Chem. 266:6416-6423(1991) [PubMed: 2007593] [Abstract] Cited for: PROTEIN SEQUENCE OF 21-32.
[5]	"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].
[6]	"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 SER-243, MASS SPECTROMETRY.
[7]	"Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences." Taylor A.B., Smith B.S., Kitada S., Kojima K., Miyaura H., Otwinowski Z., Ito A., Deisenhofer J. Structure 9:615-625(2001) [PubMed: 11470436] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 21-462 IN COMPLEX WITH ZINC AND SUBSTRATES, MUTAGENESIS OF GLU-73.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X07649 Genomic DNA. Translation: CAA30489.1.
U51921 Genomic DNA. Translation: AAB67487.1.
AY693198 Genomic DNA. Translation: AAT93217.1.

PIR

S00552.

RefSeq

NP_013264.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HR6	X-ray	2.50	B/D/F/H	21-462	[»]
1HR7	X-ray	2.55	B/D/F/H	21-462	[»]
1HR8	X-ray	2.70	B/D/F/H	21-462	[»]
1HR9	X-ray	3.01	B/D/F/H	21-462	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:2402N.

IntAct

P10507. 20 interactions.

Protein family/group databases

MEROPS

M16.003.
M16.980.

Proteomic databases

PeptideAtlas

P10507.

PRIDE

P10507.

Genome annotation databases

Ensembl

YLR163C. Saccharomyces cerevisiae. [Contig view]

GeneID

850860.

GenomeReviews

Gene locus YLR163C in contig Y13138_GR.

KEGG

sce:YLR163C.

NMPDR

fig|4932.3.peg.4273.

Organism-specific databases

CYGD

YLR163c.

SGD

S000004153. MAS1.

Yeast-GFP

Search...

Phylogenomic databases

HOGENOM

P10507.

OMA

P10507. IPLMVAN.

Enzyme and pathway databases

BRENDA

3.4.24.64. 250.

Gene expression databases

ArrayExpress

P10507.

GermOnline

YLR163C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR011237. Pept_M16_core.
IPR011765. Pept_M16_N.
IPR001431. Pept_M16_Zn_BS.
IPR007863. Peptidase_M16_C.
[Graphical view]

Gene3D

G3DSA:3.30.830.10. Pept_M16_core. 2 hits.

Pfam

PF00675. Peptidase_M16. 1 hit.
PF05193. Peptidase_M16_C. 1 hit.
[Graphical view]

PROSITE

PS00143. INSULINASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

967179.

Entry information

Entry name

MPPB_YEAST

Accession

Primary (citable) accession number: P10507

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	July 1, 1989
Last modified:	June 16, 2009
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)