P0AEK7 (FDNI_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Formate dehydrogenase, nitrate-inducible, cytochrome b556(fdn) subunit

Alternative name(s):
Anaerobic formate dehydrogenase cytochrome b556 subunit
Formate dehydrogenase-N subunit gamma
Short name=FDH-N subunit gamma

Gene names

Name:	fdnI
Ordered Locus Names:	b1476, JW1472

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	217 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. Subunit gamma is the cytochrome b556(FDN) component of the formate dehydrogenase.
Cofactor	Binds 2 heme groups per subunit. Heme 1 is located at the cytoplasmic interface, heme 2 is located at the periplasmic interface. Electrons are transferred from the periplasmic to the cytoplasmic heme.
Subunit structure	Trimer of heterotrimers, consisting of subunits alpha, beta and gamma.
Subcellular location	Cell inner membrane; Multi-pass membrane protein.
Induction	By nitrate under anaerobic conditions.
Sequence similarities	Belongs to the formate dehydrogenase gamma subunit family.

Ontologies

Keywords
Biological process	Electron transport Transport
Cellular component	Cell inner membrane Cell membrane Membrane
Domain	Transmembrane Transmembrane helix
Ligand	Heme Iron 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 cytochrome complex assembly Inferred from direct assay PubMed 1099093. Source: EcoCyc respiratory electron transport chain Inferred from electronic annotation. Source: InterPro
Cellular_component	formate dehydrogenase complex Inferred from direct assay PubMed 11752799. Source: EcoCyc integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	electron carrier activity Inferred from direct assay PubMed 1099094. Source: EcoCyc 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 – 217

217

Formate dehydrogenase, nitrate-inducible, cytochrome b556(fdn) subunit

PRO_0000087210

Regions

Topological domain

1 – 11

11

Cytoplasmic Ref.5

Transmembrane

12 – 36

25

Helical

Topological domain

37 – 52

16

Periplasmic Ref.5

Transmembrane

53 – 74

22

Helical

Topological domain

75 – 110

36

Cytoplasmic Ref.5

Transmembrane

111 – 134

24

Helical

Topological domain

135 – 150

16

Periplasmic Ref.5

Transmembrane

151 – 175

25

Helical

Topological domain

176 – 217

42

Cytoplasmic Ref.5

Sites

Metal binding

18

1

Iron (heme B 1 axial ligand)

Metal binding

57

1

Iron (heme B 2 axial ligand)

Metal binding

155

1

Iron (heme B 2 axial ligand)

Metal binding

169

1

Iron (heme B 1 axial ligand)

Experimental info

Sequence conflict

160 – 217

58

IILIH…SEEGI → YHPDPRHPDPYVYGILGERI D Ref.1

Secondary structure

1

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217

Helix Strand Turn

Details...

Beta strand

4 – 8

5

Helix

12 – 36

25

Helix

41 – 45

5

Helix

50 – 75

26

Helix

76 – 78

3

Helix

83 – 85

3

Helix

86 – 90

5

Helix

92 – 96

5

Helix

100 – 103

4

Helix

111 – 133

23

Turn

136 – 139

4

Helix

140 – 142

3

Helix

145 – 175

31

Helix

179 – 184

6

Beta strand

187 – 189

3

Helix

190 – 196

7

Helix

198 – 215

18

Sequences

	Sequence		Length	Mass (Da)
	P0AEK7 [UniParc]. Last modified December 20, 2005. Version 1. Checksum: B10073F14343515E	FASTA	217	25,368
	10 20 30 40 50 60 MSKSKMIVRT KFIDRACHWT VVICFFLVAL SGISFFFPTL QWLTQTFGTP QMGRILHPFF 70 80 90 100 110 120 GIAIFVALMF MFVRFVHHNI PDKKDIPWLL NIVEVLKGNE HKVADVGKYN AGQKMMFWSI 130 140 150 160 170 180 MSMIFVLLVT GVIIWRPYFA QYFPMQVVRY SLLIHAAAGI ILIHAILIHM YMAFWVKGSI 190 200 210 KGMIEGKVSR RWAKKHHPRW YREIEKAEAK KESEEGI

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]	"Global topology analysis of the Escherichia coli inner membrane proteome." Daley D.O., Rapp M., Granseth E., Melen K., Drew D., von Heijne G. Science 308:1321-1323(2005) [PubMed] [Europe PMC] [Abstract] Cited for: TOPOLOGY [LARGE SCALE ANALYSIS]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"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), METAL BINDING AT HIS-18; HIS-57; HIS-155 AND HIS-169.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M75029 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAD13440.1.
AP009048 Genomic DNA. Translation: BAA15125.1.

PIR

JS0630. G64900.

RefSeq

NP_415993.1. NC_000913.2.
YP_489741.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1KQF	X-ray	1.60	C	1-217	[»]
1KQG	X-ray	2.80	C	1-217	[»]

ProteinModelPortal

P0AEK7.

SMR

P0AEK7. Positions 2-217.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0AEK7. 1 interaction.

STRING

511145.b1476.

Protein family/group databases

TCDB

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

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAD13440; AAD13440; b1476.
BAA15125; BAA15125; BAA15125.

GeneID

12933909.
946038.

KEGG

ecj:Y75_p1452.
eco:b1476.

PATRIC

32118244. VBIEscCol129921_1542.

Organism-specific databases

EchoBASE

EB1211.

EcoGene

EG11229. fdnI.

Phylogenomic databases

eggNOG

COG2864.

HOGENOM

HOG000163500.

KO

K08350.

OMA

IMWRPYF.

ProtClustDB

PRK10179.

Enzyme and pathway databases

BioCyc

EcoCyc:FDNI-MONOMER.
ECOL316407:JW1472-MONOMER.
MetaCyc:FDNI-MONOMER.

Gene expression databases

Genevestigator

P0AEK7.

Family and domain databases

InterPro

IPR016174. Di-haem_cyt_TM.
IPR006471. Formate_DH_gsu.
[Graphical view]

Pfam

PF00033. Cytochrom_B_N. 1 hit.
[Graphical view]

SUPFAM

SSF81342. Transmembr_di-haem_cytochrome. 1 hit.

TIGRFAMs

TIGR01583. formate-DH-gamm. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P0AEK7.

Entry information

Entry name

FDNI_ECOLI

Accession

Primary (citable) accession number: P0AEK7
Secondary accession number(s): P24185, P77513

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	December 20, 2005
Last modified:	May 1, 2013
This is version 73 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program