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Protein

Glutaconyl-CoA decarboxylase subunit alpha

Gene

gcdA

Organism
Acidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Decarboxylase subunit of the primary sodium pump glutaconyl-CoA decarboxylase (GCD).

Catalytic activityi

4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2.

Pathway: L-glutamate degradation via hydroxyglutarate pathway

This protein is involved in step 5 of the subpathway that synthesizes crotonoyl-CoA from L-glutamate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. no protein annotated in this organism
  3. Glutaconate CoA-transferase subunit A (gctA), Glutaconate CoA-transferase subunit B (gctB)
  4. (R)-2-hydroxyglutaryl-CoA dehydratase subunit beta (hgdB), (R)-2-hydroxyglutaryl-CoA dehydratase subunit alpha (hgdA)
  5. Glutaconyl-CoA decarboxylase subunit gamma (gcdC), Glutaconyl-CoA decarboxylase subunit beta (gcdB), Glutaconyl-CoA decarboxylase subunit delta (gcdD), Glutaconyl-CoA decarboxylase subunit alpha (gcdA)
This subpathway is part of the pathway L-glutamate degradation via hydroxyglutarate pathway, which is itself part of Amino-acid degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes crotonoyl-CoA from L-glutamate, the pathway L-glutamate degradation via hydroxyglutarate pathway and in Amino-acid degradation.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Ion transport, Sodium transport, Transport

Keywords - Ligandi

Biotin, Sodium

Enzyme and pathway databases

BioCyciAFER591001:GHUL-1890-MONOMER.
MetaCyc:MONOMER-1054.
BRENDAi4.1.1.70. 85.
SABIO-RKQ06700.
UniPathwayiUPA00533; UER00688.

Protein family/group databases

TCDBi3.B.1.1.3. the na(+)-transporting carboxylic acid decarboxylase (nat-dc) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Glutaconyl-CoA decarboxylase subunit alpha (EC:4.1.1.70)
Alternative name(s):
Carboxyltransferase
Gene namesi
Name:gcdA
Ordered Locus Names:Acfer_1817
OrganismiAcidaminococcus fermentans (strain ATCC 25085 / DSM 20731 / VR4)
Taxonomic identifieri591001 [NCBI]
Taxonomic lineageiBacteriaFirmicutesNegativicutesSelenomonadalesAcidaminococcaceaeAcidaminococcus
ProteomesiUP000001902 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 587587Glutaconyl-CoA decarboxylase subunit alphaPRO_0000087438Add
BLAST

Interactioni

Subunit structurei

Heterooctamer consisting of two alpha, two beta, two gamma and two delta subunits.

Protein-protein interaction databases

STRINGi591001.Acfer_1817.

Structurei

Secondary structure

1
587
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 104Combined sources
Helixi25 – 4723Combined sources
Helixi52 – 576Combined sources
Helixi63 – 708Combined sources
Beta strandi77 – 804Combined sources
Beta strandi94 – 1029Combined sources
Beta strandi105 – 1128Combined sources
Turni114 – 1196Combined sources
Helixi125 – 13915Combined sources
Beta strandi143 – 1475Combined sources
Helixi154 – 1563Combined sources
Helixi157 – 1604Combined sources
Beta strandi161 – 1633Combined sources
Helixi169 – 17911Combined sources
Beta strandi184 – 1885Combined sources
Beta strandi190 – 1934Combined sources
Helixi195 – 2017Combined sources
Beta strandi202 – 2098Combined sources
Beta strandi213 – 2164Combined sources
Beta strandi227 – 2304Combined sources
Helixi233 – 24412Combined sources
Beta strandi252 – 2543Combined sources
Helixi255 – 2584Combined sources
Turni259 – 2613Combined sources
Beta strandi267 – 2715Combined sources
Helixi272 – 28413Combined sources
Helixi291 – 2944Combined sources
Beta strandi295 – 2973Combined sources
Helixi306 – 3083Combined sources
Helixi309 – 3124Combined sources
Helixi323 – 3286Combined sources
Helixi332 – 3343Combined sources
Beta strandi337 – 3404Combined sources
Beta strandi347 – 3548Combined sources
Beta strandi357 – 3648Combined sources
Beta strandi367 – 3693Combined sources
Helixi389 – 40416Combined sources
Beta strandi409 – 4135Combined sources
Helixi422 – 4265Combined sources
Helixi429 – 44113Combined sources
Beta strandi447 – 4515Combined sources
Beta strandi453 – 4564Combined sources
Helixi459 – 4624Combined sources
Turni469 – 4713Combined sources
Beta strandi472 – 4776Combined sources
Beta strandi482 – 4865Combined sources
Helixi488 – 50518Combined sources
Helixi511 – 52616Combined sources
Helixi530 – 5367Combined sources
Beta strandi538 – 5425Combined sources
Turni545 – 5473Combined sources
Helixi548 – 55912Combined sources
Helixi569 – 5713Combined sources
Helixi574 – 58310Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PIXX-ray2.20A/B1-587[»]
ProteinModelPortaliQ06700.
SMRiQ06700. Positions 2-587.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ06700.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini35 – 568534CarboxyltransferaseAdd
BLAST

Sequence similaritiesi

Contains 1 carboxyltransferase domain.Curated

Phylogenomic databases

HOGENOMiHOG000064887.
KOiK01615.
OMAiMHGETAA.

Family and domain databases

Gene3Di3.90.226.10. 2 hits.
InterProiIPR000022. Carboxyl_trans.
IPR029045. ClpP/crotonase-like_dom.
IPR011763. COA_CT_C.
IPR011762. COA_CT_N.
[Graphical view]
PfamiPF01039. Carboxyl_trans. 1 hit.
[Graphical view]
SUPFAMiSSF52096. SSF52096. 2 hits.
PROSITEiPS50989. COA_CT_CTER. 1 hit.
PS50980. COA_CT_NTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q06700-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGFYSMPRYF QNMPQVGKPL KKADAANEEQ LKKIEEEIHQ LIKEAQEAGK
60 70 80 90 100
ADADVNKRGE LTALQRIEKL VEPGSWRPLN TLFNPQGNKN GSVAIVKGLG
110 120 130 140 150
RVNGKWCVVV ASDNKKLAGA WVPGQAECLL RASDTAKTLH VPLVYVLNCS
160 170 180 190 200
GVKFDEQEKV YPNRRGGGTP FFRNAELNQL GIPVIVGIYG TNPAGGGYHS
210 220 230 240 250
ISPTVIIAHE KANMAVGGAG IMGGMNPKGH VDLEYANEIA DMVDRTGKTE
260 270 280 290 300
PPGAVDIHYT ETGFMREVYA SEEGVLEGIK KYVGMLPKYD PEFFRVDDPK
310 320 330 340 350
APAFPADDLY SMVPLNDKRA YDIYNVIARL FDNSELHEYK KGYGPEMVTG
360 370 380 390 400
LAKVNGLLVG VVANVQGLLM NYPEYKAAGS VGIGGKLYRQ GLVKMNEFVT
410 420 430 440 450
LCARDRLPIV WIQDTTGIDV GNDAEKAELL GLGQSLIYSI QTSHIPQFEI
460 470 480 490 500
TLRKGTAAAH YVLGGPQGND TNAFSIGTAA TEIAVMNGET AATAMYSRRL
510 520 530 540 550
AKDRKAGKDL QPTIDKMNNL IQAFYTKSRP KVCAELGLVD EIVDMNKIRG
560 570 580
YVEAFTEAAY QNPESICPFH QMILPRAIRE FETFVKK
Length:587
Mass (Da):64,347
Last modified:November 1, 1996 - v1
Checksum:iBF1C0D2F2DCA86DA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69435 Genomic DNA. Translation: CAA49210.1.
CP001859 Genomic DNA. Translation: ADB48171.1.
X59645 Genomic DNA. Translation: CAA42195.1.
PIRiS29787.
RefSeqiWP_012939154.1. NC_013740.1.
YP_003399486.1. NC_013740.1.

Genome annotation databases

EnsemblBacteriaiADB48171; ADB48171; Acfer_1817.
KEGGiafn:Acfer_1817.
PATRICi31910225. VBIAciFer109666_1808.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69435 Genomic DNA. Translation: CAA49210.1.
CP001859 Genomic DNA. Translation: ADB48171.1.
X59645 Genomic DNA. Translation: CAA42195.1.
PIRiS29787.
RefSeqiWP_012939154.1. NC_013740.1.
YP_003399486.1. NC_013740.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PIXX-ray2.20A/B1-587[»]
ProteinModelPortaliQ06700.
SMRiQ06700. Positions 2-587.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi591001.Acfer_1817.

Protein family/group databases

TCDBi3.B.1.1.3. the na(+)-transporting carboxylic acid decarboxylase (nat-dc) family.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADB48171; ADB48171; Acfer_1817.
KEGGiafn:Acfer_1817.
PATRICi31910225. VBIAciFer109666_1808.

Phylogenomic databases

HOGENOMiHOG000064887.
KOiK01615.
OMAiMHGETAA.

Enzyme and pathway databases

UniPathwayiUPA00533; UER00688.
BioCyciAFER591001:GHUL-1890-MONOMER.
MetaCyc:MONOMER-1054.
BRENDAi4.1.1.70. 85.
SABIO-RKQ06700.

Miscellaneous databases

EvolutionaryTraceiQ06700.

Family and domain databases

Gene3Di3.90.226.10. 2 hits.
InterProiIPR000022. Carboxyl_trans.
IPR029045. ClpP/crotonase-like_dom.
IPR011763. COA_CT_C.
IPR011762. COA_CT_N.
[Graphical view]
PfamiPF01039. Carboxyl_trans. 1 hit.
[Graphical view]
SUPFAMiSSF52096. SSF52096. 2 hits.
PROSITEiPS50989. COA_CT_CTER. 1 hit.
PS50980. COA_CT_NTER. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, sequencing and expression of the gene encoding the carboxytransferase subunit of the biotin-dependent Na+ pump glutaconyl-CoA decarboxylase from Acidaminococcus fermentans in Escherichia coli."
    Bendrat K., Buckel W.
    Eur. J. Biochem. 211:697-702(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 25085 / DSM 20731 / VR4.
  3. "Identification of the gene encoding the activator of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans by gene expression in Escherichia coli."
    Bendrat K., Mueller U., Klees A.-G., Buckel W.
    FEBS Lett. 329:329-331(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 548-587.
  4. "Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans."
    Mueller U., Buckel W.
    Eur. J. Biochem. 230:698-704(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 548-587.
  5. "Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase."
    Wendt K.S., Schall I., Huber R., Buckel W., Jacob U.
    EMBO J. 22:3493-3502(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).

Entry informationi

Entry nameiGCDA_ACIFV
AccessioniPrimary (citable) accession number: Q06700
Secondary accession number(s): D2RM69
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: June 24, 2015
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.