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Protein

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

Gene

sucB

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

Functioni

The 2-oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO2. It contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3).

Catalytic activityi

Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine.

Cofactori

(R)-lipoateNote: Binds 1 lipoyl cofactor covalently.

Pathwayi: L-lysine degradation via saccharopine pathway

This protein is involved in step 6 of the subpathway that synthesizes glutaryl-CoA from L-lysine.
Proteins known to be involved in the 6 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. no protein annotated in this organism
  3. no protein annotated in this organism
  4. no protein annotated in this organism
  5. no protein annotated in this organism
  6. Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (sucB)
This subpathway is part of the pathway L-lysine degradation via saccharopine 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 glutaryl-CoA from L-lysine, the pathway L-lysine degradation via saccharopine pathway and in Amino-acid degradation.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei3761
Active sitei3801

GO - Molecular functioni

  • dihydrolipoyllysine-residue succinyltransferase activity Source: EcoliWiki
  • lipoic acid binding Source: EcoliWiki

GO - Biological processi

  • L-lysine catabolic process to acetyl-CoA via saccharopine Source: UniProtKB-UniPathway
  • tricarboxylic acid cycle Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Tricarboxylic acid cycle

Enzyme and pathway databases

BioCyciEcoCyc:E2O-MONOMER.
ECOL316407:JW0716-MONOMER.
MetaCyc:E2O-MONOMER.
BRENDAi2.3.1.61. 2026.
UniPathwayiUPA00868; UER00840.

Names & Taxonomyi

Protein namesi
Recommended name:
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex (EC:2.3.1.61)
Alternative name(s):
2-oxoglutarate dehydrogenase complex component E2
Short name:
OGDC-E2
Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Gene namesi
Name:sucB
Ordered Locus Names:b0727, JW0716
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10980. sucB.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • oxoglutarate dehydrogenase complex Source: EcoliWiki
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001622622 – 405Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complexAdd BLAST404

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei44N6-lipoyllysinePROSITE-ProRule annotation1 Publication1
Modified residuei148N6-acetyllysine1 Publication1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP0AFG6.
PaxDbiP0AFG6.
PRIDEiP0AFG6.

2D gel databases

SWISS-2DPAGEP0AFG6.

Interactioni

Subunit structurei

Forms a 24-polypeptide structural core with octahedral symmetry.

Binary interactionsi

WithEntry#Exp.IntActNotes
sucAP0AFG35EBI-558621,EBI-543523

Protein-protein interaction databases

BioGridi4259945. 11 interactors.
DIPiDIP-35787N.
IntActiP0AFG6. 39 interactors.
MINTiMINT-1242608.
STRINGi511145.b0727.

Structurei

Secondary structure

1405
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi31 – 34Combined sources4
Beta strandi42 – 44Combined sources3
Beta strandi70 – 76Combined sources7
Beta strandi105 – 107Combined sources3
Helixi116 – 118Combined sources3
Helixi121 – 124Combined sources4
Helixi129 – 131Combined sources3
Beta strandi136 – 139Combined sources4
Helixi143 – 146Combined sources4
Turni147 – 149Combined sources3
Beta strandi176 – 178Combined sources3
Helixi183 – 196Combined sources14
Beta strandi201 – 209Combined sources9
Helixi211 – 228Combined sources18
Helixi235 – 248Combined sources14
Turni250 – 253Combined sources4
Beta strandi255 – 257Combined sources3
Beta strandi260 – 262Combined sources3
Beta strandi269 – 271Combined sources3
Beta strandi273 – 275Combined sources3
Beta strandi278 – 280Combined sources3
Helixi287 – 289Combined sources3
Helixi292 – 305Combined sources14
Turni306 – 309Combined sources4
Helixi313 – 316Combined sources4
Beta strandi320 – 325Combined sources6
Helixi326 – 329Combined sources4
Beta strandi343 – 358Combined sources16
Beta strandi361 – 375Combined sources15
Turni376 – 378Combined sources3
Helixi381 – 396Combined sources16
Helixi400 – 403Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BALNMR-A104-153[»]
1BBLNMR-A104-153[»]
1C4TX-ray3.00A/B/C173-405[»]
1E2OX-ray3.00A173-405[»]
1PMRNMR-A2-81[»]
1SCZX-ray2.20A173-405[»]
1W4HNMR-A109-153[»]
2BTGNMR-A109-153[»]
2BTHNMR-A109-153[»]
2WXCNMR-A109-153[»]
ProteinModelPortaliP0AFG6.
SMRiP0AFG6.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AFG6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 78Lipoyl-bindingPROSITE-ProRule annotationAdd BLAST76

Sequence similaritiesi

Belongs to the 2-oxoacid dehydrogenase family.Curated
Contains 1 lipoyl-binding domain.PROSITE-ProRule annotationCurated

Keywords - Domaini

Lipoyl

Phylogenomic databases

eggNOGiENOG4105C7S. Bacteria.
COG0508. LUCA.
HOGENOMiHOG000281563.
InParanoidiP0AFG6.
KOiK00658.
OMAiTFGKKAR.
PhylomeDBiP0AFG6.

Family and domain databases

Gene3Di3.30.559.10. 1 hit.
4.10.320.10. 1 hit.
InterProiIPR003016. 2-oxoA_DH_lipoyl-BS.
IPR001078. 2-oxoacid_DH_actylTfrase.
IPR000089. Biotin_lipoyl.
IPR023213. CAT-like_dom.
IPR004167. E3-bd.
IPR011053. Single_hybrid_motif.
IPR006255. SucB.
[Graphical view]
PfamiPF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view]
SUPFAMiSSF47005. SSF47005. 1 hit.
SSF51230. SSF51230. 1 hit.
TIGRFAMsiTIGR01347. sucB. 1 hit.
PROSITEiPS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P0AFG6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSVDILVPD LPESVADATV ATWHKKPGDA VVRDEVLVEI ETDKVVLEVP
60 70 80 90 100
ASADGILDAV LEDEGTTVTS RQILGRLREG NSAGKETSAK SEEKASTPAQ
110 120 130 140 150
RQQASLEEQN NDALSPAIRR LLAEHNLDAS AIKGTGVGGR LTREDVEKHL
160 170 180 190 200
AKAPAKESAP AAAAPAAQPA LAARSEKRVP MTRLRKRVAE RLLEAKNSTA
210 220 230 240 250
MLTTFNEVNM KPIMDLRKQY GEAFEKRHGI RLGFMSFYVK AVVEALKRYP
260 270 280 290 300
EVNASIDGDD VVYHNYFDVS MAVSTPRGLV TPVLRDVDTL GMADIEKKIK
310 320 330 340 350
ELAVKGRDGK LTVEDLTGGN FTITNGGVFG SLMSTPIINP PQSAILGMHA
360 370 380 390 400
IKDRPMAVNG QVEILPMMYL ALSYDHRLID GRESVGFLVT IKELLEDPTR

LLLDV
Length:405
Mass (Da):44,011
Last modified:January 23, 2007 - v2
Checksum:i8439E48C6D381277
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01619 Genomic DNA. Translation: AAA23898.1.
X00664 Genomic DNA. Translation: CAA25284.1.
U00096 Genomic DNA. Translation: AAC73821.1.
AP009048 Genomic DNA. Translation: BAA35393.1.
X00661 Genomic DNA. Translation: CAA25281.1.
PIRiF64808. XUECSD.
RefSeqiNP_415255.1. NC_000913.3.
WP_000099823.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73821; AAC73821; b0727.
BAA35393; BAA35393; BAA35393.
GeneIDi945307.
KEGGiecj:JW0716.
eco:b0727.
PATRICi32116649. VBIEscCol129921_0757.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01619 Genomic DNA. Translation: AAA23898.1.
X00664 Genomic DNA. Translation: CAA25284.1.
U00096 Genomic DNA. Translation: AAC73821.1.
AP009048 Genomic DNA. Translation: BAA35393.1.
X00661 Genomic DNA. Translation: CAA25281.1.
PIRiF64808. XUECSD.
RefSeqiNP_415255.1. NC_000913.3.
WP_000099823.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BALNMR-A104-153[»]
1BBLNMR-A104-153[»]
1C4TX-ray3.00A/B/C173-405[»]
1E2OX-ray3.00A173-405[»]
1PMRNMR-A2-81[»]
1SCZX-ray2.20A173-405[»]
1W4HNMR-A109-153[»]
2BTGNMR-A109-153[»]
2BTHNMR-A109-153[»]
2WXCNMR-A109-153[»]
ProteinModelPortaliP0AFG6.
SMRiP0AFG6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259945. 11 interactors.
DIPiDIP-35787N.
IntActiP0AFG6. 39 interactors.
MINTiMINT-1242608.
STRINGi511145.b0727.

2D gel databases

SWISS-2DPAGEP0AFG6.

Proteomic databases

EPDiP0AFG6.
PaxDbiP0AFG6.
PRIDEiP0AFG6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73821; AAC73821; b0727.
BAA35393; BAA35393; BAA35393.
GeneIDi945307.
KEGGiecj:JW0716.
eco:b0727.
PATRICi32116649. VBIEscCol129921_0757.

Organism-specific databases

EchoBASEiEB0973.
EcoGeneiEG10980. sucB.

Phylogenomic databases

eggNOGiENOG4105C7S. Bacteria.
COG0508. LUCA.
HOGENOMiHOG000281563.
InParanoidiP0AFG6.
KOiK00658.
OMAiTFGKKAR.
PhylomeDBiP0AFG6.

Enzyme and pathway databases

UniPathwayiUPA00868; UER00840.
BioCyciEcoCyc:E2O-MONOMER.
ECOL316407:JW0716-MONOMER.
MetaCyc:E2O-MONOMER.
BRENDAi2.3.1.61. 2026.

Miscellaneous databases

EvolutionaryTraceiP0AFG6.
PROiP0AFG6.

Family and domain databases

Gene3Di3.30.559.10. 1 hit.
4.10.320.10. 1 hit.
InterProiIPR003016. 2-oxoA_DH_lipoyl-BS.
IPR001078. 2-oxoacid_DH_actylTfrase.
IPR000089. Biotin_lipoyl.
IPR023213. CAT-like_dom.
IPR004167. E3-bd.
IPR011053. Single_hybrid_motif.
IPR006255. SucB.
[Graphical view]
PfamiPF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view]
SUPFAMiSSF47005. SSF47005. 1 hit.
SSF51230. SSF51230. 1 hit.
TIGRFAMsiTIGR01347. sucB. 1 hit.
PROSITEiPS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiODO2_ECOLI
AccessioniPrimary (citable) accession number: P0AFG6
Secondary accession number(s): P07016
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 109 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.