Q42523 (MCCA_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial
Short name=MCCase subunit alpha
EC=6.4.1.4

Alternative name(s):
3-methylcrotonyl-CoA carboxylase 1
3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha

Gene names

Name:	MCCA
Ordered Locus Names:	At1g03090
ORF Names:	F10O3.9, F10O3_8

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	734 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)

Catalytic activity	ATP + 3-methylcrotonoyl-CoA + HCO3- = ADP + phosphate + 3-methylglutaconyl-CoA.
Cofactor	Biotin. Binds 2 manganese ions per subunit By similarity.
Pathway	Amino-acid degradation; L-leucine degradation; (S)-3-hydroxy-3-methylglutaryl-CoA from 3-isovaleryl-CoA: step 2/3.
Subunit structure	Probably a heterodimer composed of biotin-containing alpha subunits and beta subunits By similarity.
Subcellular location	Mitochondrion matrix.
Tissue specificity	In roots, cotyledons, leaves, flowers, ovaries, siliques and embryos. Ref.5
Miscellaneous	Temporal and spatial accumulation of the alpha and beta subunits during development at approximately equal molar ratios.
Sequence similarities	Contains 1 ATP-grasp domain. Contains 1 biotin carboxylation domain. Contains 1 biotinyl-binding domain.
Sequence caution	The sequence AAD25800.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Cellular component	Mitochondrion
Coding sequence diversity	Alternative splicing
Domain	Transit peptide
Ligand	ATP-binding Biotin Manganese Metal-binding Nucleotide-binding
Molecular function	Ligase
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	leucine catabolic process Inferred from direct assay PubMed 12068107. Source: TAIR
Cellular_component	cytosolic ribosome Inferred from direct assay PubMed 15821981. Source: TAIR mitochondrial matrix Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion Inferred from direct assay PubMed 12068107PubMed 18385124. Source: TAIR
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW biotin carboxylase activity Inferred from electronic annotation. Source: InterPro cobalt ion binding Inferred from direct assay PubMed 20018591. Source: TAIR methylcrotonoyl-CoA carboxylase activity Inferred from direct assay PubMed 12068107. Source: TAIR
Complete GO annotation...

Alternative products

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

Isoform 1 (identifier: Q42523-1)

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 2 (identifier: Q42523-2)

The sequence of this isoform differs from the canonical sequence as follows:
     281-300: Missing.

Note: May be due to exon skipping. No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 25	25	Mitochondrion Potential
	Chain	26 – 734	709	Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial		PRO_0000002835
Regions
	Domain	37 – 484	448	Biotin carboxylation
	Domain	156 – 354	199	ATP-grasp
	Domain	665 – 732	68	Biotinyl-binding
Sites
	Active site	329	1	By similarity
	Metal binding	311	1	Manganese 1 By similarity
	Metal binding	325	1	Manganese 1 By similarity
	Metal binding	325	1	Manganese 2 By similarity
	Metal binding	327	1	Manganese 2 By similarity
	Binding site	152	1	ATP By similarity
	Binding site	236	1	ATP By similarity
	Binding site	271	1	ATP By similarity
Amino acid modifications
	Modified residue	645	1	Phosphoserine Ref.6
	Modified residue	699	1	N6-biotinyllysine By similarity
Natural variations
	Alternative sequence	281 – 300	20	Missing in isoform 2.		VSP_008910
Experimental info
	Sequence conflict	85	1	V → D in AAA67356. Ref.1
	Sequence conflict	92	1	A → AK in AAA67356. Ref.1
	Sequence conflict	430	1	W → L in AAA67356. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 2, 2002. Version 2. Checksum: 251CACF6464B046B	FASTA	734	80,451
	10 20 30 40 50 60 MSMMTVWALR RNVRRKNHSM LVRYISGSAS MKPKEQCIEK ILVANRGEIA CRIMRTAKRL 70 80 90 100 110 120 GIQTVAVYSD ADRDSLHVKS ADEAVRIGPP SARLSYLSGV TIMEAAARTG AQAIHPGYGF 130 140 150 160 170 180 LSESSDFAQL CEDSGLTFIG PPASAIRDMG DKSASKRIMG AAGVPLVPGY HGHEQDIDHM 190 200 210 220 230 240 KSEAEKIGYP IIIKPTHGGG GKGMRIVQSG KDFADSFLGA QREAAASFGV NTILLEKYIT 250 260 270 280 290 300 RPRHIEVQIF GDKHGNVLHL YERDCSVQRR HQKIIEEAPA PNISEKFRAN LGQAAVSAAR 310 320 330 340 350 360 AVGYYNAGTV EFIVDTESDQ FYFMEMNTRL QVEHPVTEMI VGQDLVEWQI RVANGEPLPL 370 380 390 400 410 420 SQSEVPMSGH AFEARIYAEN VPKGFLPATG VLNHYRPVAV SPSVRVETGV EQGDTVSMHY 430 440 450 460 470 480 DPMIAKLVVW GGNRGEALVK LKDCLSNFQV AGVPTNINFL QKLASHKEFA VGNVETHFIE 490 500 510 520 530 540 HHKSDLFADE SNPAATEVAY KAVKHSAALV AACISTIEHS TWNESNHGKV PSIWYSNPPF 550 560 570 580 590 600 RVHHEAKQTI ELEWNNECEG TGSNLISLGV RYQPDGSYLI EEGNDSPSLE LRVTRAGKCD 610 620 630 640 650 660 FRVEAAGLSM NVSLAAYLKD GYKHIHIWHG SEHHQFKQKV GIEFSEDEEG VQHRTSSETS 670 680 690 700 710 720 SHPPGTIVAP MAGLVVKVLV ENEAKVDQGQ PILVLEAMKM EHVVKAPSSG SIQDLKVKAG 730 QQVSDGSALF RIKG
	Isoform 2 [UniParc]. Checksum: 60AE5054E7C1C9E2	FASTA	714	78,369
	10 20 30 40 50 60 MSMMTVWALR RNVRRKNHSM LVRYISGSAS MKPKEQCIEK ILVANRGEIA CRIMRTAKRL 70 80 90 100 110 120 GIQTVAVYSD ADRDSLHVKS ADEAVRIGPP SARLSYLSGV TIMEAAARTG AQAIHPGYGF 130 140 150 160 170 180 LSESSDFAQL CEDSGLTFIG PPASAIRDMG DKSASKRIMG AAGVPLVPGY HGHEQDIDHM 190 200 210 220 230 240 KSEAEKIGYP IIIKPTHGGG GKGMRIVQSG KDFADSFLGA QREAAASFGV NTILLEKYIT 250 260 270 280 290 300 RPRHIEVQIF GDKHGNVLHL YERDCSVQRR HQKIIEEAPA AVGYYNAGTV EFIVDTESDQ 310 320 330 340 350 360 FYFMEMNTRL QVEHPVTEMI VGQDLVEWQI RVANGEPLPL SQSEVPMSGH AFEARIYAEN 370 380 390 400 410 420 VPKGFLPATG VLNHYRPVAV SPSVRVETGV EQGDTVSMHY DPMIAKLVVW GGNRGEALVK 430 440 450 460 470 480 LKDCLSNFQV AGVPTNINFL QKLASHKEFA VGNVETHFIE HHKSDLFADE SNPAATEVAY 490 500 510 520 530 540 KAVKHSAALV AACISTIEHS TWNESNHGKV PSIWYSNPPF RVHHEAKQTI ELEWNNECEG 550 560 570 580 590 600 TGSNLISLGV RYQPDGSYLI EEGNDSPSLE LRVTRAGKCD FRVEAAGLSM NVSLAAYLKD 610 620 630 640 650 660 GYKHIHIWHG SEHHQFKQKV GIEFSEDEEG VQHRTSSETS SHPPGTIVAP MAGLVVKVLV 670 680 690 700 710 ENEAKVDQGQ PILVLEAMKM EHVVKAPSSG SIQDLKVKAG QQVSDGSALF RIKG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning of the biotinylated subunit of 3-methylcrotonyl-coenzyme A carboxylase of Arabidopsis thaliana." Weaver L.M., Lebrun L., Franklin A., Huang L., Hoffman N., Wurtele E.S., Nikolau B.J. Plant Physiol. 107:1013-1014(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2). Strain: cv. Columbia.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: cv. Columbia.
[5]	"Molecular characterization of the non-biotin-containing subunit of 3-methylcrotonyl-CoA carboxylase." McKean A.L., Ke J., Song J., Che P., Achenbach S., Nikolau B.J., Wurtele E.S. J. Biol. Chem. 275:5582-5590(2000) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY. Strain: cv. Columbia and cv. Landsberg erecta.
[6]	"Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks." Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A., Grossmann J., Gruissem W., Baginsky S. Plant Physiol. 150:889-903(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-645, MASS SPECTROMETRY. Strain: cv. Columbia. Tissue: Seedling.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U12536 mRNA. Translation: AAA67356.1. AC006550 Genomic DNA. Translation: AAD25800.1. Sequence problems. CP002684 Genomic DNA. Translation: AEE27527.1. CP002684 Genomic DNA. Translation: AEE27528.1. AY070723 mRNA. Translation: AAL50065.1.
IPI	IPI00539641. IPI00544747.
PIR	G86161.
RefSeq	NP_563674.1. NM_100191.3. NP_849583.1. NM_179252.2.
UniGene	At.24059.
3D structure databases
ProteinModelPortal	Q42523.
SMR	Q42523. Positions 36-487, 665-717.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT1G03090.2-P.
Proteomic databases
PaxDb	Q42523.
PRIDE	Q42523.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G03090.2; AT1G03090.2; AT1G03090.
GeneID	838362.
KEGG	ath:AT1G03090.
Organism-specific databases
TAIR	At1g03090.
Phylogenomic databases
eggNOG	COG4770.
HOGENOM	HOG000008989.
InParanoid	Q42523.
KO	K01968.
OMA	CRDERRC.
PhylomeDB	Q42523.
ProtClustDB	CLSN2916952.
Enzyme and pathway databases
BRENDA	6.4.1.4. 401.
UniPathway	UPA00363; UER00861.
Gene expression databases
Genevestigator	Q42523.
GermOnline	AT1G03090. Arabidopsis thaliana.
Family and domain databases
Gene3D	3.30.1490.20. 1 hit. 3.30.470.20. 1 hit. 3.40.50.20. 1 hit.
InterPro	IPR011761. ATP-grasp. IPR013815. ATP_grasp_subdomain_1. IPR013816. ATP_grasp_subdomain_2. IPR001882. Biotin_BS. IPR011764. Biotin_carboxylation_dom. IPR005482. Biotin_COase_C. IPR000089. Biotin_lipoyl. IPR005481. CarbamoylP_synth_lsu_N. IPR005479. CbamoylP_synth_lsu-like_ATP-bd. IPR016185. PreATP-grasp_dom. IPR011054. Rudment_hybrid_motif. IPR011053. Single_hybrid_motif. [Graphical view]
Pfam	PF02785. Biotin_carb_C. 1 hit. PF00364. Biotin_lipoyl. 1 hit. PF00289. CPSase_L_chain. 1 hit. PF02786. CPSase_L_D2. 1 hit. [Graphical view]
SMART	SM00878. Biotin_carb_C. 1 hit. [Graphical view]
SUPFAM	SSF51230. Hybrid_motif. 1 hit. SSF52440. PreATP-grasp-like. 1 hit. SSF51246. Rudmnt_hyb_motif. 1 hit.
PROSITE	PS50975. ATP_GRASP. 1 hit. PS50979. BC. 1 hit. PS00188. BIOTIN. 1 hit. PS50968. BIOTINYL_LIPOYL. 1 hit. PS00866. CPSASE_1. 1 hit. PS00867. CPSASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

MCCA_ARATH

Accession

Primary (citable) accession number: Q42523
Secondary accession number(s): Q9SA61

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 2, 2002
Last sequence update:	May 2, 2002
Last modified:	May 1, 2013
This is version 126 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program