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Protein

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

Gene

sucB

Organism
Azotobacter vinelandii
Status
Reviewed-Annotation score: Annotation score: 4 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 3 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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei370 – 3701By similarity
Active sitei374 – 3741By similarity

GO - Molecular functioni

  1. dihydrolipoyllysine-residue succinyltransferase activity Source: UniProtKB-EC

GO - Biological processi

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

Keywords - Molecular functioni

Acyltransferase, Transferase

Keywords - Biological processi

Tricarboxylic acid cycle

Enzyme and pathway databases

BRENDAi2.3.1.61. 49.
SABIO-RKP20708.
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
Synonyms:odhB
OrganismiAzotobacter vinelandii
Taxonomic identifieri354 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaeAzotobacter

Subcellular locationi

GO - Cellular componenti

  1. oxoglutarate dehydrogenase complex Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 399398Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complexPRO_0000162255Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei43 – 431N6-lipoyllysinePROSITE-ProRule annotation

Proteomic databases

PRIDEiP20708.

Interactioni

Subunit structurei

Forms a 24-polypeptide structural core with octahedral symmetry.

Structurei

Secondary structure

1
399
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 64Combined sources
Beta strandi17 – 193Combined sources
Beta strandi28 – 303Combined sources
Beta strandi35 – 406Combined sources
Beta strandi45 – 495Combined sources
Beta strandi54 – 618Combined sources
Beta strandi72 – 765Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GHJNMR-A2-80[»]
1GHKNMR-A2-80[»]
ProteinModelPortaliP20708.
SMRiP20708. Positions 2-80, 167-399.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP20708.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 7776Lipoyl-bindingPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Keywords - Domaini

Lipoyl

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.

P20708-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAIDIKAPTF PESIADGTVA TWHKKPGEPV KRDELIVDIE TDKVVMEVLA
60 70 80 90 100
EADGVIAEIV KNEGDTVLSG ELLGKLTEGG AATAAPAAAP APAAAAPAAA
110 120 130 140 150
EAPILSPAAR KIAEENAIAA DSITGTGKGG RVTKEDAVAA AEAKKSAPAG
160 170 180 190 200
QPAPAATAAP LFAAGDRVEK RVPMTRLRAK VAERLVEAQS SMAMLTTFNE
210 220 230 240 250
VNMKPVMELR AKYKDLFEKT HNGVRLGFMS FFVKAAVEAL KRQPGVNASI
260 270 280 290 300
DGNDIVYHGY QDIGVAVSSD RGLVVPVLRN AEFMSLAEIE GGINEFGKKA
310 320 330 340 350
KAGKLTIEEM TGGTFTISNG GVFGSLLSTP IVNPPQTAIL GMHKIQERPM
360 370 380 390
AVNGQVVILP MMYLALSYDH RLIDGKEAVT FLVTMKDLLE DPARLLLDV
Length:399
Mass (Da):42,003
Last modified:January 23, 2007 - v2
Checksum:i3A801A1B519E73D3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M37307 Genomic DNA. Translation: AAA22138.1. Sequence problems.
X52432 Genomic DNA. Translation: CAA36678.1.
X52433 Genomic DNA. Translation: CAA36681.1.
PIRiS07779.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M37307 Genomic DNA. Translation: AAA22138.1. Sequence problems.
X52432 Genomic DNA. Translation: CAA36678.1.
X52433 Genomic DNA. Translation: CAA36681.1.
PIRiS07779.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GHJNMR-A2-80[»]
1GHKNMR-A2-80[»]
ProteinModelPortaliP20708.
SMRiP20708. Positions 2-80, 167-399.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP20708.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00868; UER00840.
BRENDAi2.3.1.61. 49.
SABIO-RKP20708.

Miscellaneous databases

EvolutionaryTraceiP20708.

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...

Publicationsi

  1. "The 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. 2. Molecular cloning and sequence analysis of the gene encoding the succinyltransferase component."
    Westphal A.H., de Kok A.
    Eur. J. Biochem. 187:235-239(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 478 / NRS 16 / DSM 2289 / VKM B-1617.
  2. "Lipoamide dehydrogenase from Azotobacter vinelandii. Molecular cloning, organization and sequence analysis of the gene."
    Westphal A.H., de Kok A.
    Eur. J. Biochem. 172:299-305(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 354-399.
    Strain: ATCC 478 / NRS 16 / DSM 2289 / VKM B-1617.
  3. "The 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. 1. Molecular cloning and sequence analysis of the gene encoding the 2-oxoglutarate dehydrogenase component."
    Schulze E., Westphal A.H., Hanemaaijer R., de Kok A.
    Eur. J. Biochem. 187:229-234(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-30.
    Strain: ATCC 478 / NRS 16 / DSM 2289 / VKM B-1617.
  4. "Sequential 1H and 15N nuclear magnetic resonance assignments and secondary structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii. Evidence for high structural similarity with the lipoyl domain of the pyruvate dehydrogenase complex."
    Berg A., Smits O., de Kok A., Vervoort J.
    Eur. J. Biochem. 234:148-159(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-80.
  5. "Solution structure of the lipoyl domain of the 2-oxoglutarate dehydrogenase complex from Azotobacter vinelandii."
    Berg A., Vervoort J., de Kok A.
    J. Mol. Biol. 261:432-442(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-78.

Entry informationi

Entry nameiODO2_AZOVI
AccessioniPrimary (citable) accession number: P20708
Secondary accession number(s): Q44474
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 105 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

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.