P33224 (AIDB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Putative acyl-CoA dehydrogenase AidB
EC=1.3.99.-

Gene names

Name:	aidB
Ordered Locus Names:	b4187, JW5867

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	541 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Part of the adaptive DNA-repair response to alkylating agents. Could prevent alkylation damage by protecting DNA and destroying alkylating agents that have yet to reach their DNA target. Binds to double-stranded DNA with a preference for a DNA region that includes its own promoter. Shows weak isovaleryl-CoA dehydrogenase activity in vitro. Ref.1 Ref.5 Ref.7
Cofactor	FAD. Ref.5 Ref.7 Binds one FAD per subunit. Ref.5 Ref.7
Subunit structure	Homotetramer. Dimer of dimers. Ref.5 Ref.7
Subcellular location	Cytoplasm Potential.
Induction	Regulated by Ada in response to alkylating agents. Also induced by anaerobiosis or by acetate at pH 6.5, via RpoS. Represses its own synthesis during normal cell growth. Ref.1 Ref.6
Domain	The N-terminal region contains FAD-dependent dehydrogenase activity and the C-terminal region contains DNA-binding activity. Ref.6
Sequence similarities	Belongs to the acyl-CoA dehydrogenase family.
Sequence caution	The sequence AAA97083.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened. The sequence AAC18889.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Stress response
Cellular component	Cytoplasm
Ligand	DNA-binding FAD Flavoprotein
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	cellular response to stress Inferred from expression pattern. Source: EcoCyc
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	isovaleryl-CoA dehydrogenase activity Inferred from direct assay Ref.5. Source: EcoCyc sequence-specific DNA binding Inferred from direct assay Ref.6. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 541

541

Putative acyl-CoA dehydrogenase AidB

PRO_0000201192

Regions

Nucleotide binding

182 – 191

10

FAD

Nucleotide binding

216 – 218

3

FAD

Nucleotide binding

423 – 433

11

FAD

Region

445 – 541

97

dsDNA-binding

Sites

Binding site

185

1

FAD

Binding site

191

1

FAD

Binding site

218

1

FAD

Binding site

429

1

FAD

Experimental info

Mutagenesis

437

1

R → Q: Does not affect DNA binding affinity. Ref.7

Mutagenesis

518

1

R → Q: Reduces DNA binding affinity. Ref.7

Secondary structure

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541

Helix Strand Turn

Details...

Turn

20 – 23

4

Helix

27 – 33

7

Helix

40 – 45

6

Helix

53 – 57

5

Helix

61 – 64

4

Beta strand

68 – 72

5

Beta strand

78 – 83

6

Helix

86 – 97

12

Turn

98 – 102

5

Helix

103 – 105

3

Helix

114 – 127

14

Helix

132 – 148

17

Helix

151 – 156

6

Helix

157 – 160

4

Helix

193 – 195

3

Beta strand

199 – 202

4

Beta strand

208 – 211

4

Beta strand

214 – 218

5

Beta strand

222 – 230

9

Beta strand

236 – 243

8

Beta strand

251 – 257

7

Beta strand

268 – 276

9

Helix

298 – 303

6

Helix

307 – 323

17

Helix

331 – 333

3

Helix

335 – 348

14

Helix

352 – 363

12

Turn

364 – 366

3

Helix

368 – 387

20

Helix

391 – 399

9

Helix

411 – 423

13

Helix

430 – 441

12

Helix

446 – 454

9

Helix

461 – 473

13

Helix

484 – 491

8

Helix

497 – 501

5

Helix

504 – 515

12

Helix

525 – 534

10

Sequences

	Sequence		Length	Mass (Da)
	P33224 [UniParc]. Last modified December 1, 2000. Version 3. Checksum: D609E364E3A99208	FASTA	541	60,590
	10 20 30 40 50 60 MHWQTHTVFN QPIPLNNSNL YLSDGALCEA VTREGAGWDS DFLASIGQQL GTAESLELGR 70 80 90 100 110 120 LANVNPPELL RYDAQGRRLD DVRFHPAWHL LMQALCTNRV HNLAWEEDAR SGAFVARAAR 130 140 150 160 170 180 FMLHAQVEAG SLCPITMTFA ATPLLLQMLP APFQDWTTPL LSDRYDSHLL PGGQKRGLLI 190 200 210 220 230 240 GMGMTEKQGG SDVMSNTTRA ERLEDGSYRL VGHKWFFSVP QSDAHLVLAQ TAGGLSCFFV 250 260 270 280 290 300 PRFLPDGQRN AIRLERLKDK LGNRSNASCE VEFQDAIGWL LGLEGEGIRL ILKMGGMTRF 310 320 330 340 350 360 DCALGSHAMM RRAFSLAIYH AHQRHVFGNP LIQQPLMRHV LSRMALQLEG QTALLFRLAR 370 380 390 400 410 420 AWDRRADAKE ALWARLFTPA AKFVICKRGM PFVAEAMEVL GGIGYCEESE LPRLYREMPV 430 440 450 460 470 480 NSIWEGSGNI MCLDVLRVLN KQAGVYDLLS EAFVEVKGQD RYFDRAVRRL QQQLRKPAEE 490 500 510 520 530 540 LGREITHQLF LLGCGAQMLK YASPPMAQAW CQVMLDTRGG VRLSEQIQND LLLRATGGVC V

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and transcriptional regulation of the Escherichia coli adaptive response gene aidB." Landini P., Hajec L.I., Volkert M.R. J. Bacteriol. 176:6583-6589(1994) [PubMed: 7961409] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION. Strain: K12 / MV1161.
[2]	"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes." Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R. Nucleic Acids Res. 23:2105-2119(1995) [PubMed: 7610040] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein." Rohankhedkar M.S., Mulrooney S.B., Wedemeyer W.J., Hausinger R.P. J. Bacteriol. 188:223-230(2006) [PubMed: 16352838] [Abstract] Cited for: PROTEIN SEQUENCE OF 195-204, FUNCTION, DNA-BINDING, COFACTOR, SUBUNIT. Strain: K12.
[6]	"Specific DNA binding and regulation of its own expression by the AidB protein in Escherichia coli." Rippa V., Amoresano A., Esposito C., Landini P., Volkert M., Duilio A. J. Bacteriol. 192:6136-6142(2010) [PubMed: 20889740] [Abstract] Cited for: DNA-BINDING, DOMAIN, AUTOREGULATION, INDUCTION. Strain: K12.
[7]	"Structure and DNA binding of alkylation response protein AidB." Bowles T., Metz A.H., O'Quin J., Wawrzak Z., Eichman B.F. Proc. Natl. Acad. Sci. U.S.A. 105:15299-15304(2008) [PubMed: 18829440] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH FAD, FUNCTION, COFACTOR, SUBUNIT, MUTAGENESIS OF ARG-437 AND ARG-518.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L20915 Genomic DNA. Translation: AAC18889.1. Different initiation.
L20915 Genomic DNA. Translation: AAC18890.1.
U14003 Genomic DNA. Translation: AAA97083.1. Different initiation.
U00096 Genomic DNA. Translation: AAC77144.2.
AP009048 Genomic DNA. Translation: BAE78188.1.

PIR

I41124.

RefSeq

NP_418608.6. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3DJL	X-ray	1.70	A	1-541	[»]
3U33	X-ray	2.80	A/B/C/D/E/F/G/H/I/J/K/L	1-541	[»]

ProteinModelPortal

P33224.

SMR

P33224. Positions 3-540.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9078N.

IntAct

P33224. 32 interactions.

MINT

MINT-1221527.

Proteomic databases

PRIDE

P33224.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000000949; EBESCP00000000949; EBESCG00000000779.
EBESCT00000017042; EBESCP00000016333; EBESCG00000016101.

GeneID

948710.

GenomeReviews

Gene locus JW5867 in contig AP009048_GR.
Gene locus b4187 in contig U00096_GR.

KEGG

ecj:JW5867.
eco:b4187.

PATRIC

32123949. VBIEscCol129921_4319.

Organism-specific databases

EchoBASE

EB1759.

EcoGene

EG11811. aidB.

Phylogenomic databases

eggNOG

COG1960.

GeneTree

EBGT00050000008857.

HOGENOM

HBG569787.

OMA

RGALAWM.

PhylomeDB

P33224.

ProtClustDB

PRK11561.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11811-MONOMER.
MetaCyc:EG11811-MONOMER.

Gene expression databases

Genevestigator

P33224.

Family and domain databases

InterPro

IPR006089. Acyl-CoA_DH_CS.
IPR006090. Acyl-CoA_Oxase/DH_1.
IPR006091. Acyl-CoA_Oxase/DH_cen-dom.
IPR009075. AcylCo_DH/oxidase_C.
IPR009100. AcylCoA_DH/oxidase.
[Graphical view]

Gene3D

G3DSA:2.40.110.10. Acyl_CoA_DH/ox_M. 1 hit.
G3DSA:1.20.140.10. AcylCoA_DH_1/2_C. 1 hit.

KO

K09456.

Pfam

PF00441. Acyl-CoA_dh_1. 1 hit.
PF02770. Acyl-CoA_dh_M. 1 hit.
[Graphical view]

SUPFAM

SSF56645. AcylCoA_dehyd_NM. 1 hit.
SSF47203. AcylCoADH_C_like. 1 hit.

PROSITE

PS00072. ACYL_COA_DH_1. 1 hit.
PS00073. ACYL_COA_DH_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

AIDB_ECOLI

Accession

Primary (citable) accession number: P33224
Secondary accession number(s): P33223, Q2M6B8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1994
Last sequence update:	December 1, 2000
Last modified:	January 25, 2012
This is version 99 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program