P20708 (ODO2_AZOVI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	sucB
Synonyms:	odhB

Organism

Azotobacter vinelandii

Taxonomic identifier

354 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Azotobacter group › Azotobacter

Protein attributes

Sequence length	399 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine.
Cofactor	Binds 1 lipoyl cofactor covalently.
Pathway	Amino-acid degradation; L-lysine degradation via saccharopine pathway; glutaryl-CoA from L-lysine: step 6/6.
Subunit structure	Forms a 24-polypeptide structural core with octahedral symmetry.
Sequence similarities	Belongs to the 2-oxoacid dehydrogenase family. Contains 1 lipoyl-binding domain.

Ontologies

Keywords
Biological process	Tricarboxylic acid cycle
Domain	Lipoyl
Molecular function	Acyltransferase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	L-lysine catabolic process to acetyl-CoA via saccharopine Inferred from electronic annotation. Source: UniProtKB-UniPathway tricarboxylic acid cycle Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	oxoglutarate dehydrogenase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	dihydrolipoyllysine-residue succinyltransferase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 399

398

Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex

PRO_0000162255

Regions

Domain

2 – 76

75

Lipoyl-binding

Sites

Active site

370

1

By similarity

Active site

374

1

By similarity

Amino acid modifications

Modified residue

43

1

N6-lipoyllysine Potential

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

399

Helix Strand Turn

Details...

Beta strand

3 – 6

4

Beta strand

17 – 19

3

Beta strand

28 – 30

3

Beta strand

35 – 40

6

Beta strand

45 – 49

5

Beta strand

54 – 61

8

Beta strand

72 – 76

5

Sequences

	Sequence		Length	Mass (Da)
	P20708 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 3A801A1B519E73D3	FASTA	399	42,003
	10 20 30 40 50 60 MAIDIKAPTF PESIADGTVA TWHKKPGEPV KRDELIVDIE TDKVVMEVLA EADGVIAEIV 70 80 90 100 110 120 KNEGDTVLSG ELLGKLTEGG AATAAPAAAP APAAAAPAAA EAPILSPAAR KIAEENAIAA 130 140 150 160 170 180 DSITGTGKGG RVTKEDAVAA AEAKKSAPAG QPAPAATAAP LFAAGDRVEK RVPMTRLRAK 190 200 210 220 230 240 VAERLVEAQS SMAMLTTFNE VNMKPVMELR AKYKDLFEKT HNGVRLGFMS FFVKAAVEAL 250 260 270 280 290 300 KRQPGVNASI DGNDIVYHGY QDIGVAVSSD RGLVVPVLRN AEFMSLAEIE GGINEFGKKA 310 320 330 340 350 360 KAGKLTIEEM TGGTFTISNG GVFGSLLSTP IVNPPQTAIL GMHKIQERPM AVNGQVVILP 370 380 390 MMYLALSYDH RLIDGKEAVT FLVTMKDLLE DPARLLLDV

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M37307 Genomic DNA. Translation: AAA22138.1. Sequence problems.
X52432 Genomic DNA. Translation: CAA36678.1.
X52433 Genomic DNA. Translation: CAA36681.1.

PIR

S07779.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GHJ	NMR	-	A	2-80	[»]
1GHK	NMR	-	A	2-80	[»]

ProteinModelPortal

P20708.

SMR

P20708. Positions 2-80, 167-399.

ModBase

Search...

Proteomic databases

PRIDE

P20708.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BRENDA

2.3.1.61. 49.

SABIO-RK

P20708.

UniPathway

UPA00868; UER00840.

Family and domain databases

Gene3D

3.30.559.10. 1 hit.
4.10.320.10. 1 hit.

InterPro

IPR003016. 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]

Pfam

PF00198. 2-oxoacid_dh. 1 hit.
PF00364. Biotin_lipoyl. 1 hit.
PF02817. E3_binding. 1 hit.
[Graphical view]

SUPFAM

SSF47005. E3_bd. 1 hit.
SSF51230. Hybrid_motif. 1 hit.

TIGRFAMs

TIGR01347. sucB. 1 hit.

PROSITE

PS50968. BIOTINYL_LIPOYL. 1 hit.
PS00189. LIPOYL. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P20708.

Entry information

Entry name

ODO2_AZOVI

Accession

Primary (citable) accession number: P20708
Secondary accession number(s): Q44474

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 102 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program