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Protein

Glyoxylate carboligase

Gene

gcl

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the condensation of two molecules of glyoxylate to give 2-hydroxy-3-oxopropanoate (also termed tartronate semialdehyde).

Catalytic activityi

2 glyoxylate = tartronate semialdehyde + CO2.

Cofactori

Protein has several cofactor binding sites:
  • Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity
  • thiamine diphosphateBy similarityNote: Binds 1 thiamine pyrophosphate per subunit.By similarity

Pathwayi: glycolate degradation

This protein is involved in step 2 of the subpathway that synthesizes 3-phospho-D-glycerate from glycolate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Glyoxylate carboligase (gcl)
  3. 2-hydroxy-3-oxopropionate reductase (glxR)
  4. Glycerate kinase (glxK)
This subpathway is part of the pathway glycolate degradation, which is itself part of Organic acid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 3-phospho-D-glycerate from glycolate, the pathway glycolate degradation and in Organic acid metabolism.

GO - Molecular functioni

  • FAD binding Source: EcoCyc
  • identical protein binding Source: EcoCyc
  • magnesium ion binding Source: InterPro
  • tartronate-semialdehyde synthase activity Source: EcoCyc
  • thiamine pyrophosphate binding Source: EcoCyc

GO - Biological processi

  • glycolate catabolic process Source: EcoCyc
  • glyoxylate catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Magnesium, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciEcoCyc:GLYOCARBOLIG-MONOMER.
ECOL316407:JW0495-MONOMER.
MetaCyc:GLYOCARBOLIG-MONOMER.
BRENDAi4.1.1.47. 2165.
UniPathwayiUPA00864; UER00831.

Names & Taxonomyi

Protein namesi
Recommended name:
Glyoxylate carboligase (EC:4.1.1.47)
Alternative name(s):
Tartronate-semialdehyde synthase
Gene namesi
Name:gcl
Ordered Locus Names:b0507, JW0495
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11583. gcl.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 593592Glyoxylate carboligasePRO_0000090832Add
BLAST

Proteomic databases

EPDiP0AEP7.
PaxDbiP0AEP7.
PRIDEiP0AEP7.

Expressioni

Inductioni

By glyoxylate.

Interactioni

Subunit structurei

Homotetramer.

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4263336. 2 interactions.
DIPiDIP-48112N.
IntActiP0AEP7. 6 interactions.
MINTiMINT-1302810.
STRINGi511145.b0507.

Structurei

Secondary structure

1
593
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 53Combined sources
Helixi6 – 1611Combined sources
Beta strandi21 – 244Combined sources
Helixi28 – 303Combined sources
Helixi31 – 4010Combined sources
Beta strandi44 – 474Combined sources
Helixi51 – 6414Combined sources
Beta strandi70 – 745Combined sources
Helixi78 – 814Combined sources
Helixi84 – 929Combined sources
Beta strandi97 – 1037Combined sources
Helixi106 – 1083Combined sources
Turni109 – 1124Combined sources
Helixi119 – 1235Combined sources
Helixi124 – 1263Combined sources
Beta strandi127 – 1326Combined sources
Helixi136 – 1383Combined sources
Helixi139 – 15113Combined sources
Beta strandi152 – 1543Combined sources
Beta strandi158 – 1636Combined sources
Helixi164 – 1685Combined sources
Beta strandi169 – 1724Combined sources
Helixi175 – 1773Combined sources
Helixi190 – 20112Combined sources
Beta strandi204 – 2107Combined sources
Helixi212 – 2165Combined sources
Helixi220 – 23011Combined sources
Beta strandi234 – 2363Combined sources
Turni238 – 2425Combined sources
Beta strandi256 – 2594Combined sources
Helixi262 – 2709Combined sources
Beta strandi272 – 2787Combined sources
Helixi283 – 2864Combined sources
Helixi289 – 2935Combined sources
Beta strandi297 – 3037Combined sources
Helixi305 – 3073Combined sources
Beta strandi310 – 3123Combined sources
Helixi322 – 33817Combined sources
Helixi346 – 35611Combined sources
Beta strandi359 – 3613Combined sources
Beta strandi368 – 3703Combined sources
Helixi372 – 38211Combined sources
Beta strandi387 – 3915Combined sources
Helixi395 – 4039Combined sources
Beta strandi411 – 4144Combined sources
Turni416 – 4183Combined sources
Helixi424 – 43411Combined sources
Beta strandi439 – 4457Combined sources
Helixi446 – 4516Combined sources
Helixi453 – 4553Combined sources
Helixi456 – 4616Combined sources
Beta strandi467 – 4726Combined sources
Helixi477 – 4826Combined sources
Helixi483 – 4864Combined sources
Helixi502 – 5043Combined sources
Helixi511 – 5177Combined sources
Beta strandi521 – 5255Combined sources
Helixi528 – 5303Combined sources
Helixi531 – 54515Combined sources
Beta strandi549 – 5557Combined sources
Helixi567 – 5693Combined sources
Beta strandi576 – 5794Combined sources
Turni580 – 5823Combined sources
Turni587 – 5893Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PANX-ray2.70A/B/C/D/E/F1-593[»]
ProteinModelPortaliP0AEP7.
SMRiP0AEP7. Positions 2-593.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AEP7.

Family & Domainsi

Sequence similaritiesi

Belongs to the TPP enzyme family.Curated

Phylogenomic databases

eggNOGiENOG41060W2. Bacteria.
COG3960. LUCA.
HOGENOMiHOG000258449.
InParanoidiP0AEP7.
KOiK01608.
OMAiWGAIPDD.
OrthoDBiEOG6KT2K7.
PhylomeDBiP0AEP7.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR006397. Glyox_carbo_lig.
IPR029061. THDP-binding.
IPR012000. Thiamin_PyroP_enz_cen_dom.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PANTHERiPTHR18968:SF14. PTHR18968:SF14. 1 hit.
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF00205. TPP_enzyme_M. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR01504. glyox_carbo_lig. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AEP7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKMRAVDAA MYVLEKEGIT TAFGVPGAAI NPFYSAMRKH GGIRHILARH
60 70 80 90 100
VEGASHMAEG YTRATAGNIG VCLGTSGPAG TDMITALYSA SADSIPILCI
110 120 130 140 150
TGQAPRARLH KEDFQAVDIE AIAKPVSKMA VTVREAALVP RVLQQAFHLM
160 170 180 190 200
RSGRPGPVLV DLPFDVQVAE IEFDPDMYEP LPVYKPAASR MQIEKAVEML
210 220 230 240 250
IQAERPVIVA GGGVINADAA ALLQQFAELT SVPVIPTLMG WGCIPDDHEL
260 270 280 290 300
MAGMVGLQTA HRYGNATLLA SDMVFGIGNR FANRHTGSVE KYTEGRKIVH
310 320 330 340 350
IDIEPTQIGR VLCPDLGIVS DAKAALTLLV EVAQEMQKAG RLPCRKEWVA
360 370 380 390 400
DCQQRKRTLL RKTHFDNVPV KPQRVYEEMN KAFGRDVCYV TTIGLSQIAA
410 420 430 440 450
AQMLHVFKDR HWINCGQAGP LGWTIPAALG VCAADPKRNV VAISGDFDFQ
460 470 480 490 500
FLIEELAVGA QFNIPYIHVL VNNAYLGLIR QSQRAFDMDY CVQLAFENIN
510 520 530 540 550
SSEVNGYGVD HVKVAEGLGC KAIRVFKPED IAPAFEQAKA LMAQYRVPVV
560 570 580 590
VEVILERVTN ISMGSELDNV MEFEDIADNA ADAPTETCFM HYE
Length:593
Mass (Da):64,732
Last modified:January 23, 2007 - v2
Checksum:iEF35ECC43B7C62E7
GO

Sequence cautioni

The sequence AAB40260.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L03845 Genomic DNA. Translation: AAA23864.1.
U82664 Genomic DNA. Translation: AAB40260.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73609.1.
AP009048 Genomic DNA. Translation: BAE76285.1.
PIRiJT0742.
RefSeqiNP_415040.1. NC_000913.3.
WP_001096881.1. NZ_CP014272.1.

Genome annotation databases

EnsemblBacteriaiAAC73609; AAC73609; b0507.
BAE76285; BAE76285; BAE76285.
GeneIDi945394.
KEGGiecj:JW0495.
eco:b0507.
PATRICi32116173. VBIEscCol129921_0528.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L03845 Genomic DNA. Translation: AAA23864.1.
U82664 Genomic DNA. Translation: AAB40260.1. Different initiation.
U00096 Genomic DNA. Translation: AAC73609.1.
AP009048 Genomic DNA. Translation: BAE76285.1.
PIRiJT0742.
RefSeqiNP_415040.1. NC_000913.3.
WP_001096881.1. NZ_CP014272.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PANX-ray2.70A/B/C/D/E/F1-593[»]
ProteinModelPortaliP0AEP7.
SMRiP0AEP7. Positions 2-593.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263336. 2 interactions.
DIPiDIP-48112N.
IntActiP0AEP7. 6 interactions.
MINTiMINT-1302810.
STRINGi511145.b0507.

Proteomic databases

EPDiP0AEP7.
PaxDbiP0AEP7.
PRIDEiP0AEP7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73609; AAC73609; b0507.
BAE76285; BAE76285; BAE76285.
GeneIDi945394.
KEGGiecj:JW0495.
eco:b0507.
PATRICi32116173. VBIEscCol129921_0528.

Organism-specific databases

EchoBASEiEB1542.
EcoGeneiEG11583. gcl.

Phylogenomic databases

eggNOGiENOG41060W2. Bacteria.
COG3960. LUCA.
HOGENOMiHOG000258449.
InParanoidiP0AEP7.
KOiK01608.
OMAiWGAIPDD.
OrthoDBiEOG6KT2K7.
PhylomeDBiP0AEP7.

Enzyme and pathway databases

UniPathwayiUPA00864; UER00831.
BioCyciEcoCyc:GLYOCARBOLIG-MONOMER.
ECOL316407:JW0495-MONOMER.
MetaCyc:GLYOCARBOLIG-MONOMER.
BRENDAi4.1.1.47. 2165.

Miscellaneous databases

EvolutionaryTraceiP0AEP7.
PROiP0AEP7.

Family and domain databases

Gene3Di3.40.50.1220. 1 hit.
3.40.50.970. 2 hits.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR006397. Glyox_carbo_lig.
IPR029061. THDP-binding.
IPR012000. Thiamin_PyroP_enz_cen_dom.
IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
IPR011766. TPP_enzyme-bd_C.
[Graphical view]
PANTHERiPTHR18968:SF14. PTHR18968:SF14. 1 hit.
PfamiPF02775. TPP_enzyme_C. 1 hit.
PF00205. TPP_enzyme_M. 1 hit.
PF02776. TPP_enzyme_N. 1 hit.
[Graphical view]
SUPFAMiSSF52467. SSF52467. 1 hit.
SSF52518. SSF52518. 2 hits.
TIGRFAMsiTIGR01504. glyox_carbo_lig. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular cloning, DNA sequencing, and biochemical analyses of Escherichia coli glyoxylate carboligase. An enzyme of the acetohydroxy acid synthase-pyruvate oxidase family."
    Chang Y.-Y., Wang A.-Y., Cronan J.E. Jr.
    J. Biol. Chem. 268:3911-3919(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-31.
    Strain: K12.
  2. "Sequence of minutes 4-25 of Escherichia coli."
    Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M., Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D., Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.
    Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.

Entry informationi

Entry nameiGCL_ECOLI
AccessioniPrimary (citable) accession number: P0AEP7
Secondary accession number(s): P30146, P77126, Q2MBS1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 82 of the entry and version 2 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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 one 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.