PCCA_RUEPO
ID PCCA_RUEPO Reviewed; 681 AA.
AC Q5LUF3;
DT 13-NOV-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=Propionyl-CoA carboxylase alpha chain {ECO:0000305|PubMed:20725044};
DE EC=6.4.1.3 {ECO:0000269|PubMed:20725044};
GN Name=pccA {ECO:0000312|EMBL:AAV94401.1};
GN OrderedLocusNames=SPO1101 {ECO:0000312|EMBL:AAV94401.1};
OS Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (Silicibacter
OS pomeroyi).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Roseobacteraceae; Ruegeria.
OX NCBI_TaxID=246200;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=15602564; DOI=10.1038/nature03170;
RA Moran M.A., Buchan A., Gonzalez J.M., Heidelberg J.F., Whitman W.B.,
RA Kiene R.P., Henriksen J.R., King G.M., Belas R., Fuqua C., Brinkac L.M.,
RA Lewis M., Johri S., Weaver B., Pai G., Eisen J.A., Rahe E., Sheldon W.M.,
RA Ye W., Miller T.R., Carlton J., Rasko D.A., Paulsen I.T., Ren Q.,
RA Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R.,
RA Nelson W.C., Sullivan S.A., Rosovitz M.J., Haft D.H., Selengut J., Ward N.;
RT "Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine
RT environment.";
RL Nature 432:910-913(2004).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 700808 / DSM 15171 / DSS-3;
RX PubMed=25780504; DOI=10.1186/1944-3277-9-11;
RA Rivers A.R., Smith C.B., Moran M.A.;
RT "An updated genome annotation for the model marine bacterium Ruegeria
RT pomeroyi DSS-3.";
RL Stand. Genomic Sci. 9:11-11(2014).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) IN COMPLEX WITH BETA SUBUNIT FROM
RP ROSEOBACTER AND BIOTIN, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, PATHWAY,
RP SUBUNIT, DOMAIN, BIOTINYLATION AT LYS-647, AND MUTAGENESIS OF TRP-515;
RP LEU-599; LEU-602 AND MET-603.
RX PubMed=20725044; DOI=10.1038/nature09302;
RA Huang C.S., Sadre-Bazzaz K., Shen Y., Deng B., Zhou Z.H., Tong L.;
RT "Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme
RT A carboxylase.";
RL Nature 466:1001-1005(2010).
CC -!- FUNCTION: This is one of the 2 subunits of the biotin-dependent
CC propionyl-CoA carboxylase (PCC), the enzyme catalyzing the
CC carboxylation of propionyl-CoA/propanoyl-CoA to D-methylmalonyl-
CC CoA/(S)-methylmalonyl-CoA (PubMed:20725044). Within the holoenzyme, the
CC alpha subunit catalyzes the ATP-dependent carboxylation of the biotin
CC carried by the biotin carboxyl carrier (BCC) domain, while the beta
CC subunit then tranfers the carboxyl group from carboxylated biotin to
CC propionyl-CoA (Probable). {ECO:0000269|PubMed:20725044,
CC ECO:0000305|PubMed:20725044}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + hydrogencarbonate + propanoyl-CoA = (S)-methylmalonyl-
CC CoA + ADP + H(+) + phosphate; Xref=Rhea:RHEA:23720,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:17544, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57327, ChEBI:CHEBI:57392,
CC ChEBI:CHEBI:456216; EC=6.4.1.3;
CC Evidence={ECO:0000269|PubMed:20725044};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:23721;
CC Evidence={ECO:0000269|PubMed:20725044};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00409,
CC ECO:0000255|PROSITE-ProRule:PRU00969};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00409,
CC ECO:0000255|PROSITE-ProRule:PRU00969};
CC Note=Binds 2 magnesium or manganese ions per subunit.
CC {ECO:0000255|PROSITE-ProRule:PRU00409, ECO:0000255|PROSITE-
CC ProRule:PRU00969};
CC -!- COFACTOR:
CC Name=biotin; Xref=ChEBI:CHEBI:57586;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU01066,
CC ECO:0000269|PubMed:20725044};
CC -!- PATHWAY: Metabolic intermediate metabolism; propanoyl-CoA degradation;
CC succinyl-CoA from propanoyl-CoA: step 1/3.
CC {ECO:0000305|PubMed:20725044}.
CC -!- SUBUNIT: The holoenzyme is a dodecamer composed of 6 PccA/alpha
CC subunits and 6 PccB/beta subunits. {ECO:0000269|PubMed:20725044}.
CC -!- INTERACTION:
CC Q5LUF3; Q5LUG0: pccB; NbExp=3; IntAct=EBI-9023176, EBI-15871336;
CC Q5LUF3; Q168G2: pccB; Xeno; NbExp=3; IntAct=EBI-9023176, EBI-9023183;
CC -!- DOMAIN: Consists of an N-terminal biotin carboxylation/carboxylase (BC)
CC domain that catalyzes the transient carboxylation of the biotin
CC covalently attached to the C-terminal biotinyl-binding/biotin carboxyl
CC carrier (BCC) domain. {ECO:0000305|PubMed:20725044}.
CC -!- PTM: The biotin cofactor is covalently attached to the C-terminal
CC biotinyl-binding domain and is required for the catalytic activity.
CC {ECO:0000269|PubMed:20725044}.
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DR EMBL; CP000031; AAV94401.1; -; Genomic_DNA.
DR RefSeq; WP_011046848.1; NC_003911.12.
DR PDB; 3N6R; X-ray; 3.20 A; A/C/E/G/I/K=1-681.
DR PDBsum; 3N6R; -.
DR AlphaFoldDB; Q5LUF3; -.
DR SMR; Q5LUF3; -.
DR DIP; DIP-59242N; -.
DR IntAct; Q5LUF3; 2.
DR STRING; 246200.SPO1101; -.
DR DNASU; 3193848; -.
DR EnsemblBacteria; AAV94401; AAV94401; SPO1101.
DR KEGG; sil:SPO1101; -.
DR eggNOG; COG4770; Bacteria.
DR HOGENOM; CLU_000395_3_3_5; -.
DR OMA; HEIQVTC; -.
DR OrthoDB; 361205at2; -.
DR BRENDA; 6.4.1.3; 8123.
DR UniPathway; UPA00945; UER00908.
DR EvolutionaryTrace; Q5LUF3; -.
DR Proteomes; UP000001023; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004658; F:propionyl-CoA carboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0016042; P:lipid catabolic process; IEA:UniProtKB-KW.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR005481; BC-like_N.
DR InterPro; IPR001882; Biotin_BS.
DR InterPro; IPR011764; Biotin_carboxylation_dom.
DR InterPro; IPR005482; Biotin_COase_C.
DR InterPro; IPR000089; Biotin_lipoyl.
DR InterPro; IPR005479; CbamoylP_synth_lsu-like_ATP-bd.
DR InterPro; IPR041265; PCC_BT.
DR InterPro; IPR016185; PreATP-grasp_dom_sf.
DR InterPro; IPR011054; Rudment_hybrid_motif.
DR InterPro; IPR011053; Single_hybrid_motif.
DR Pfam; PF02785; Biotin_carb_C; 1.
DR Pfam; PF00289; Biotin_carb_N; 1.
DR Pfam; PF00364; Biotin_lipoyl; 1.
DR Pfam; PF02786; CPSase_L_D2; 1.
DR Pfam; PF18140; PCC_BT; 1.
DR SMART; SM00878; Biotin_carb_C; 1.
DR SUPFAM; SSF51230; SSF51230; 1.
DR SUPFAM; SSF51246; SSF51246; 1.
DR SUPFAM; SSF52440; SSF52440; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
DR PROSITE; PS50979; BC; 1.
DR PROSITE; PS00188; BIOTIN; 1.
DR PROSITE; PS50968; BIOTINYL_LIPOYL; 1.
DR PROSITE; PS00866; CPSASE_1; 1.
DR PROSITE; PS00867; CPSASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Biotin; Ligase; Lipid degradation;
KW Lipid metabolism; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..681
FT /note="Propionyl-CoA carboxylase alpha chain"
FT /id="PRO_0000448576"
FT DOMAIN 1..466
FT /note="Biotin carboxylation"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00969"
FT DOMAIN 120..317
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT DOMAIN 602..681
FT /note="Biotinyl-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01066"
FT ACT_SITE 288
FT /evidence="ECO:0000250"
FT BINDING 116
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 148..209
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409"
FT BINDING 200
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 235
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 275
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 288
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 288
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 288
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 288
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 290
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 290
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00409,
FT ECO:0000255|PROSITE-ProRule:PRU00969"
FT BINDING 348
FT /ligand="biotin"
FT /ligand_id="ChEBI:CHEBI:57586"
FT /evidence="ECO:0000269|PubMed:20725044,
FT ECO:0007744|PDB:3N6R"
FT MOD_RES 647
FT /note="N6-biotinyllysine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01066,
FT ECO:0000269|PubMed:20725044, ECO:0007744|PDB:3N6R"
FT MUTAGEN 515
FT /note="W->L: No effect on holoenzyme formation."
FT /evidence="ECO:0000269|PubMed:20725044"
FT MUTAGEN 599
FT /note="L->A: Loss of holoenzyme formation; when associated
FT with A-602 and A-603."
FT /evidence="ECO:0000269|PubMed:20725044"
FT MUTAGEN 602
FT /note="L->A: Loss of holoenzyme formation; when associated
FT with A-602 and A-603."
FT /evidence="ECO:0000269|PubMed:20725044"
FT MUTAGEN 603
FT /note="M->A: No effect on holoenzyme formation. Loss of
FT holoenzyme formation; when associated with A-602 and A-
FT 603."
FT /evidence="ECO:0000269|PubMed:20725044"
FT HELIX 11..21
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 40..44
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 52..55
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 63..72
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 89..96
FT /evidence="ECO:0007829|PDB:3N6R"
FT TURN 97..99
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 107..112
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 116..124
FT /evidence="ECO:0007829|PDB:3N6R"
FT TURN 125..127
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 141..151
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 153..159
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 174..184
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 207..214
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 217..219
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 222..228
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 249..264
FT /evidence="ECO:0007829|PDB:3N6R"
FT TURN 265..267
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 270..278
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 288..290
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 297..304
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 308..316
FT /evidence="ECO:0007829|PDB:3N6R"
FT TURN 325..327
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 332..343
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 344..346
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 386..391
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 405..415
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 416..429
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 439..447
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 449..453
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 460..464
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 476..497
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 513..518
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 523..530
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 535..539
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 544..549
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 556..562
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 565..574
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 577..581
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 587..592
FT /evidence="ECO:0007829|PDB:3N6R"
FT HELIX 594..600
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 613..616
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 621..626
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 639..644
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 649..653
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 655..663
FT /evidence="ECO:0007829|PDB:3N6R"
FT STRAND 676..680
FT /evidence="ECO:0007829|PDB:3N6R"
SQ SEQUENCE 681 AA; 73862 MW; E9621118EF90D008 CRC64;
MFNKILIANR GEIACRVIKT ARKMGISTVA IYSDADKQAL HVQMADEAVH IGPPPANQSY
IVIDKVMAAI RATGAQAVHP GYGFLSENSK FAEALEAEGV IFVGPPKGAI EAMGDKITSK
KIAQEANVST VPGYMGLIED ADEAVKISNQ IGYPVMIKAS AGGGGKGMRI AWNDQEAREG
FQSSKNEAAN SFGDDRIFIE KFVTQPRHIE IQVLCDSHGN GIYLGERECS IQRRNQKVVE
EAPSPFLDEA TRRAMGEQAV ALAKAVGYAS AGTVEFIVDG QKNFYFLEMN TRLQVEHPVT
ELITGVDLVE QMIRVAAGEP LSITQGDVKL TGWAIENRLY AEDPYRGFLP SIGRLTRYRP
PAETAAGPLL VNGKWQGDAP SGEAAVRNDT GVYEGGEISM YYDPMIAKLC TWAPTRAAAI
EAMRIALDSF EVEGIGHNLP FLSAVMDHPK FISGDMTTAF IAEEYPEGFE GVNLPETDLR
RVAAAAAAMH RVAEIRRTRV SGRMDNHERR VGTEWVVTLQ GADFPVTIAA DHDGSTVSFD
DGSSMRVTSD WTPGDQLANL MVDGAPLVLK VGKISGGFRI RTRGADLKVH VRTPRQAELA
RLMPEKLPPD TSKMLLCPMP GLIVKVDVEV GQEVQEGQAL CTIEAMKMEN ILRAEKKGVV
AKINASAGNS LAVDDVIMEF E
