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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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11583. gcl.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00000908322 – 593Glyoxylate carboligaseAdd BLAST592

Proteomic databases

PaxDbiP0AEP7.
PRIDEiP0AEP7.

Expressioni

Inductioni

By glyoxylate.

Interactioni

Subunit structurei

Homotetramer.

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

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

Structurei

Secondary structure

1593
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 5Combined sources3
Helixi6 – 16Combined sources11
Beta strandi21 – 24Combined sources4
Helixi28 – 30Combined sources3
Helixi31 – 40Combined sources10
Beta strandi44 – 47Combined sources4
Helixi51 – 64Combined sources14
Beta strandi70 – 74Combined sources5
Helixi78 – 81Combined sources4
Helixi84 – 92Combined sources9
Beta strandi97 – 103Combined sources7
Helixi106 – 108Combined sources3
Turni109 – 112Combined sources4
Helixi119 – 123Combined sources5
Helixi124 – 126Combined sources3
Beta strandi127 – 132Combined sources6
Helixi136 – 138Combined sources3
Helixi139 – 151Combined sources13
Beta strandi152 – 154Combined sources3
Beta strandi158 – 163Combined sources6
Helixi164 – 168Combined sources5
Beta strandi169 – 172Combined sources4
Helixi175 – 177Combined sources3
Helixi190 – 201Combined sources12
Beta strandi204 – 210Combined sources7
Helixi212 – 216Combined sources5
Helixi220 – 230Combined sources11
Beta strandi234 – 236Combined sources3
Turni238 – 242Combined sources5
Beta strandi256 – 259Combined sources4
Helixi262 – 270Combined sources9
Beta strandi272 – 278Combined sources7
Helixi283 – 286Combined sources4
Helixi289 – 293Combined sources5
Beta strandi297 – 303Combined sources7
Helixi305 – 307Combined sources3
Beta strandi310 – 312Combined sources3
Helixi322 – 338Combined sources17
Helixi346 – 356Combined sources11
Beta strandi359 – 361Combined sources3
Beta strandi368 – 370Combined sources3
Helixi372 – 382Combined sources11
Beta strandi387 – 391Combined sources5
Helixi395 – 403Combined sources9
Beta strandi411 – 414Combined sources4
Turni416 – 418Combined sources3
Helixi424 – 434Combined sources11
Beta strandi439 – 445Combined sources7
Helixi446 – 451Combined sources6
Helixi453 – 455Combined sources3
Helixi456 – 461Combined sources6
Beta strandi467 – 472Combined sources6
Helixi477 – 482Combined sources6
Helixi483 – 486Combined sources4
Helixi502 – 504Combined sources3
Helixi511 – 517Combined sources7
Beta strandi521 – 525Combined sources5
Helixi528 – 530Combined sources3
Helixi531 – 545Combined sources15
Beta strandi549 – 555Combined sources7
Helixi567 – 569Combined sources3
Beta strandi576 – 579Combined sources4
Turni580 – 582Combined sources3
Turni587 – 589Combined sources3

3D structure databases

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

Protein-protein interaction databases

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

Proteomic databases

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.
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...

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: November 2, 2016
This is version 84 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.