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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: 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 sitei370By similarity1
Active sitei374By similarity1

GO - Molecular functioni

GO - Biological processi

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

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001622552 – 399Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complexAdd BLAST398

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei43N6-lipoyllysinePROSITE-ProRule annotation1

Proteomic databases

PRIDEiP20708.

Interactioni

Subunit structurei

Forms a 24-polypeptide structural core with octahedral symmetry.

Protein-protein interaction databases

STRINGi322710.Avin_29760.

Structurei

Secondary structure

1399
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 6Combined sources4
Beta strandi17 – 19Combined sources3
Beta strandi28 – 30Combined sources3
Beta strandi35 – 40Combined sources6
Beta strandi45 – 49Combined sources5
Beta strandi54 – 61Combined sources8
Beta strandi72 – 76Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GHJNMR-A2-80[»]
1GHKNMR-A2-80[»]
ProteinModelPortaliP20708.
SMRiP20708.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP20708.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 77Lipoyl-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.

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1GHJNMR-A2-80[»]
1GHKNMR-A2-80[»]
ProteinModelPortaliP20708.
SMRiP20708.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi322710.Avin_29760.

Proteomic databases

PRIDEiP20708.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105C7S. Bacteria.
COG0508. LUCA.

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...

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 2, 2016
This is version 111 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

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.