P0AAJ3 (FDNH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit

Alternative name(s):
Anaerobic formate dehydrogenase iron-sulfur subunit
Formate dehydrogenase-N subunit beta
Short name=FDH-N subunit beta

Gene names

Name:	fdnH
Ordered Locus Names:	b1475, JW1471

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	294 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Formate dehydrogenase allows E.coli to use formate as major electron donor during anaerobic respiration, when nitrate is used as electron acceptor. The beta chain is an electron transfer unit containing 4 cysteine clusters involved in the formation of iron-sulfur centers. Electrons are transferred from the gamma chain to the molybdenum cofactor of the alpha subunit.
Cofactor	Binds 4 4Fe-4S clusters per subunit.
Subunit structure	Trimer of heterotrimers, consisting of subunits alpha, beta and gamma.
Subcellular location	Cell membrane; Single-pass membrane protein.
Induction	By nitrate under anaerobic conditions.
Miscellaneous	The 4Fe-4S clusters from Ref.5 are renumbered in standard order.
Sequence similarities	Contains 4 4Fe-4S ferredoxin-type domains.

Ontologies

Keywords
Biological process	Electron transport Transport
Cellular component	Cell membrane Membrane
Domain	Repeat Transmembrane Transmembrane helix
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	anaerobic respiration Inferred from direct assay PubMed 1099093. Source: EcoCyc electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	formate dehydrogenase complex Inferred from direct assay PubMed 11752799. Source: EcoCyc integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW electron carrier activity Inferred from electronic annotation. Source: InterPro formate dehydrogenase (NAD+) activity Inferred from direct assay PubMed 11752799. Source: EcoCyc metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 294

294

Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit

PRO_0000159247

Regions

Topological domain

1 – 256

256

Periplasmic

Transmembrane

257 – 279

23

Helical

Topological domain

280 – 294

15

Cytoplasmic

Domain

30 – 58

29

4Fe-4S ferredoxin-type 1

Domain

91 – 123

33

4Fe-4S ferredoxin-type 2

Domain

124 – 153

30

4Fe-4S ferredoxin-type 3

Domain

158 – 189

32

4Fe-4S ferredoxin-type 4

Sites

Metal binding

39

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

42

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

45

1

Iron-sulfur 1 (4Fe-4S)

Metal binding

49

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

100

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

103

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

108

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

112

1

Iron-sulfur 4 (4Fe-4S)

Metal binding

133

1

Iron-sulfur 4 (4Fe-4S)

Metal binding

136

1

Iron-sulfur 4 (4Fe-4S)

Metal binding

139

1

Iron-sulfur 4 (4Fe-4S)

Metal binding

143

1

Iron-sulfur 3 (4Fe-4S)

Metal binding

160

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

163

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

175

1

Iron-sulfur 2 (4Fe-4S)

Metal binding

179

1

Iron-sulfur 1 (4Fe-4S)

Experimental info

Sequence conflict

101 – 102

2

MH → ID Ref.1

Secondary structure

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294

Helix Strand Turn

Details...

Beta strand

8 – 11

4

Beta strand

30 – 35

6

Turn

36 – 38

3

Helix

44 – 53

10

Beta strand

63 – 66

4

Beta strand

69 – 71

3

Beta strand

79 – 85

7

Beta strand

92 – 99

8

Beta strand

103 – 105

3

Helix

107 – 111

5

Beta strand

117 – 121

5

Beta strand

126 – 128

3

Helix

130 – 132

3

Helix

138 – 142

5

Turn

152 – 154

3

Helix

164 – 167

4

Turn

168 – 170

3

Helix

174 – 178

5

Beta strand

184 – 188

5

Helix

189 – 205

17

Beta strand

212 – 214

3

Helix

217 – 219

3

Beta strand

222 – 228

7

Turn

229 – 232

4

Helix

234 – 236

3

Turn

237 – 239

3

Helix

248 – 254

7

Helix

257 – 279

23

Sequences

	Sequence		Length	Mass (Da)
	P0AAJ3 [UniParc]. Last modified October 11, 2005. Version 1. Checksum: 44F361F4AC0AEF36	FASTA	294	32,239
	10 20 30 40 50 60 MAMETQDIIK RSATNSITPP SQVRDYKAEV AKLIDVSTCI GCKACQVACS EWNDIRDEVG 70 80 90 100 110 120 HCVGVYDNPA DLSAKSWTVM RFSETEQNGK LEWLIRKDGC MHCEDPGCLK ACPSAGAIIQ 130 140 150 160 170 180 YANGIVDFQS ENCIGCGYCI AGCPFNIPRL NKEDNRVYKC TLCVDRVSVG QEPACVKTCP 190 200 210 220 230 240 TGAIHFGTKK EMLELAEQRV AKLKARGYEH AGVYNPEGVG GTHVMYVLHH ADQPELYHGL 250 260 270 280 290 PKDPKIDTSV SLWKGALKPL AAAGFIATFA GLIFHYIGIG PNKEVDDDEE DHHE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nitrate-inducible formate dehydrogenase in Escherichia coli K-12. I. Nucleotide sequence of the fdnGHI operon and evidence that opal (UGA) encodes selenocysteine." Berg B.L., Li J., Heider J., Stewart V. J. Biol. Chem. 266:22380-22385(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Molecular basis of proton motive force generation: structure of formate dehydrogenase-N." Jormakka M., Tornroth S., Byrne B., Iwata S. Science 295:1863-1868(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M75029 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAD13439.1.
AP009048 Genomic DNA. Translation: BAA15124.1.

PIR

JS0629. F64900.

RefSeq

NP_415992.1. NC_000913.2.
YP_489740.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KQF	X-ray	1.60	B	1-294	[»]
1KQG	X-ray	2.80	B	1-294	[»]

ProteinModelPortal

P0AAJ3.

SMR

P0AAJ3. Positions 2-290.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-35836N.

IntAct

P0AAJ3. 18 interactions.

MINT

MINT-1286317.

STRING

511145.b1475.

Protein family/group databases

TCDB

5.A.3.2.1. prokaryotic molybdopterin-containing oxidoreductase (PMO) family.

Proteomic databases

PRIDE

P0AAJ3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAD13439; AAD13439; b1475.
BAA15124; BAA15124; BAA15124.

GeneID

12933907.
948794.

KEGG

ecj:Y75_p1451.
eco:b1475.

PATRIC

32118242. VBIEscCol129921_1541.

Organism-specific databases

EchoBASE

EB1210.

EcoGene

EG11228. fdnH.

Phylogenomic databases

eggNOG

COG0437.

HOGENOM

HOG000163382.

KO

K08349.

OMA

PRARDYK.

ProtClustDB

CLSK2393194.

Enzyme and pathway databases

BioCyc

EcoCyc:FDNH-MONOMER.
ECOL316407:JW1471-MONOMER.
MetaCyc:FDNH-MONOMER.

Gene expression databases

Genevestigator

P0AAJ3.

Family and domain databases

InterPro

IPR001450. 4Fe4S-bd_dom.
IPR017896. 4Fe4S_Fe-S-bd.
IPR017900. 4Fe4S_Fe_S_CS.
IPR006470. Formate_DH_bsu.
IPR014603. Formate_DH_Fe-S_su.
IPR015246. Formate_DH_TM.
[Graphical view]

Pfam

PF00037. Fer4. 1 hit.
PF12798. Fer4_3. 1 hit.
PF12838. Fer4_7. 1 hit.
PF09163. Form-deh_trans. 1 hit.
[Graphical view]

PIRSF

PIRSF036298. FDH_4Fe4S. 1 hit.

TIGRFAMs

TIGR01582. FDH-beta. 1 hit.

PROSITE

PS00198. 4FE4S_FER_1. 1 hit.
PS51379. 4FE4S_FER_2. 4 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0AAJ3.

Entry information

Entry name

FDNH_ECOLI

Accession

Primary (citable) accession number: P0AAJ3
Secondary accession number(s): P24184, P77166

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2005
Last sequence update:	October 11, 2005
Last modified:	May 1, 2013
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program