Reviewed, UniProtKB/Swiss-Prot P07658 (FDHF_ECOLI)

Names and origin

Protein names

Recommended name:
    Formate dehydrogenase H
    EC=1.2.1.2
Alternative name(s):
    Formate-hydrogen-lyase-linked, selenocysteine-containing polypeptide
    Formate dehydrogenase-H subunit alpha
      Short name=FDH-H

Gene names

Name:	fdhF
Ordered Locus Names:	b4079, JW4040

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	715 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Decomposes formic acid to hydrogen and carbon dioxide under anaerobic conditions in the absence of exogenous electron acceptors.
Catalytic activity	Formate + NAD+ = CO2 + NADH.
Cofactor	Binds 2 molybdopterin guanine dinucleotide (MGD) per subunit. Binds 1 4Fe-4S cluster per subunit. Binds 1 molybdenum ion per subunit.
Subunit structure	Consists of two separable enzymatic activities: a formate dehydrogenase component (FDH-H) and hydrogenase-3.
Induction	By formate. Repressed by oxygen, nitrate, nitrite, and other electron acceptors.
Sequence similarities	Belongs to the prokaryotic molybdopterin-containing oxidoreductase family.

Ontologies

Keywords
Coding sequence diversity	Selenocysteine
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding Molybdenum NAD Selenium
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	formate metabolic process Inferred from electronic annotation. Source: InterPro oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	formate dehydrogenase complex Inferred from electronic annotation. Source: InterPro
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 activity Inferred from electronic annotation. Source: EC iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW molybdenum ion binding Inferred from electronic annotation. Source: UniProtKB-KW selenium 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 – 715

715

Formate dehydrogenase H

PRO_0000063221

Sites

Metal binding

8

1

Iron-sulfur (4Fe-4S) By similarity

Metal binding

11

1

Iron-sulfur (4Fe-4S) By similarity

Metal binding

15

1

Iron-sulfur (4Fe-4S) By similarity

Metal binding

42

1

Iron-sulfur (4Fe-4S) By similarity

Amino acid modifications

Non-standard residue

140

1

Selenocysteine Ref.6

Experimental info

Sequence conflict

19

1

L → V in AAA23754. Ref.1

Secondary structure

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715

Helix Strand Turn

Details...

Beta strand

2 – 7

6

Beta strand

9 – 11

3

Beta strand

16 – 22

7

Beta strand

25 – 31

7

Turn

35 – 39

5

Helix

43 – 47

5

Helix

50 – 53

4

Beta strand

57 – 59

3

Helix

80 – 98

19

Helix

100 – 102

3

Beta strand

103 – 106

4

Helix

114 – 126

13

Beta strand

143 – 145

3

Helix

148 – 152

5

Helix

161 – 166

6

Beta strand

168 – 174

7

Helix

177 – 180

4

Helix

182 – 193

12

Beta strand

197 – 201

5

Helix

207 – 210

4

Beta strand

213 – 216

4

Helix

223 – 236

14

Helix

242 – 248

7

Helix

252 – 260

9

Helix

265 – 267

3

Helix

268 – 271

4

Helix

275 – 287

13

Beta strand

288 – 296

9

Helix

299 – 301

3

Beta strand

302 – 304

3

Helix

305 – 318

14

Beta strand

322 – 324

3

Beta strand

328 – 332

5

Helix

338 – 343

6

Helix

352 – 354

3

Helix

360 – 369

10

Helix

383 – 385

3

Helix

386 – 391

6

Beta strand

397 – 402

6

Helix

405 – 408

4

Beta strand

409 – 411

3

Helix

412 – 421

10

Beta strand

422 – 431

10

Helix

434 – 437

4

Beta strand

440 – 445

6

Beta strand

453 – 456

4

Beta strand

460 – 465

6

Beta strand

472 – 474

3

Helix

478 – 488

11

Helix

498 – 508

11

Turn

510 – 514

5

Helix

517 – 520

4

Turn

521 – 523

3

Beta strand

526 – 528

3

Beta strand

541 – 543

3

Beta strand

571 – 573

3

Beta strand

575 – 579

5

Helix

592 – 594

3

Helix

596 – 599

4

Beta strand

607 – 611

5

Helix

612 – 618

7

Beta strand

625 – 629

5

Beta strand

634 – 645

12

Beta strand

649 – 652

4

Beta strand

681 – 687

7

Helix

691 – 713

23

Sequences

	Sequence		Length	Mass (Da)
	P07658-1 [UniParc]. Last modified February 26, 2008. Version 2. Checksum: C7C86F6F704A142D	FASTA	715	79,374
	10 20 30 40 50 60 MKKVVTVCPY CASGCKINLV VDNGKIVRAE AAQGKTNQGT LCLKGYYGWD FINDTQILTP 70 80 90 100 110 120 RLKTPMIRRQ RGGKLEPVSW DEALNYVAER LSAIKEKYGP DAIQTTGSSR GTGNETNYVM 130 140 150 160 170 180 QKFARAVIGT NNVDCCARVU HGPSVAGLHQ SVGNGAMSNA INEIDNTDLV FVFGYNPADS 190 200 210 220 230 240 HPIVANHVIN AKRNGAKIIV CDPRKIETAR IADMHIALKN GSNIALLNAM GHVIIEENLY 250 260 270 280 290 300 DKAFVASRTE GFEEYRKIVE GYTPESVEDI TGVSASEIRQ AARMYAQAKS AAILWGMGVT 310 320 330 340 350 360 QFYQGVETVR SLTSLAMLTG NLGKPHAGVN PVRGQNNVQG ACDMGALPDT YPGYQYVKDP 370 380 390 400 410 420 ANREKFAKAW GVESLPAHTG YRISELPHRA AHGEVRAAYI MGEDPLQTDA ELSAVRKAFE 430 440 450 460 470 480 DLELVIVQDI FMTKTASAAD VILPSTSWGE HEGVFTAADR GFQRFFKAVE PKWDLKTDWQ 490 500 510 520 530 540 IISEIATRMG YPMHYNNTQE IWDELRHLCP DFYGATYEKM GELGFIQWPC RDTSDADQGT 550 560 570 580 590 600 SYLFKEKFDT PNGLAQFFTC DWVAPIDKLT DEYPMVLSTV REVGHYSCRS MTGNCAALAA 610 620 630 640 650 660 LADEPGYAQI NTEDAKRLGI EDEALVWVHS RKGKIITRAQ VSDRPNKGAI YMTYQWWIGA 670 680 690 700 710 CNELVTENLS PITKTPEYKY CAVRVEPIAD QRAAEQYVID EYNKLKTRLR EAALA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli." Zinoni F., Birkmann A., Stadtman T.C., Boeck A. Proc. Natl. Acad. Sci. U.S.A. 83:4650-4654(1986) [PubMed: 2941757] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[2]	"Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L. Nucleic Acids Res. 21:5408-5417(1993) [PubMed: 8265357] [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]	"Escherichia coli formate-hydrogen lyase. Purification and properties of the selenium-dependent formate dehydrogenase component." Axley M.J., Grahame D.A., Stadtman T.C. J. Biol. Chem. 265:18213-18218(1990) [PubMed: 2211698] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-12, CHARACTERIZATION.
[6]	"Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster." Boyington J.C., Gladyshev V.N., Khangulov S.V., Stadtman T.C., Sun P.D. Science 275:1305-1308(1997) [PubMed: 9036855] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), SELENOCYSTEINE AT SEC-140.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M13563 Genomic DNA. Translation: AAA23754.2.
U00006 Genomic DNA. Translation: AAC43173.2.
U00096 Genomic DNA. Translation: AAD13462.1.
AP009048 Genomic DNA. Translation: BAE78081.1.

PIR

DEECFS. A24145.

RefSeq

AP_004580.1.
NP_418503.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AA6	X-ray	2.30	A	1-715	[»]
1FDI	X-ray	2.90	A	1-715	[»]
1FDO	X-ray	2.80	A	1-715	[»]
2IV2	X-ray	2.27	X	1-715	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P07658.

Genome annotation databases

GeneID

948584.

GenomeReviews

Gene locus JW4040 in contig AP009048_GR.
Gene locus b4079 in contig U00096_GR.

KEGG

ecj:JW4040.
eco:b4079.

Organism-specific databases

EchoBASE

EB0281.

EcoGene

EG10285. fdhF.

CMR

Search...

Phylogenomic databases

HOGENOM

P07658.

OMA

IKNRTKG.

Enzyme and pathway databases

BioCyc

EcoCyc:FORMATEDEHYDROGH-MON.
MetaCyc:FORMATEDEHYDROGH-MON.

Gene expression databases

Genevestigator

P07658.

Family and domain databases

InterPro

IPR009010. Asp_de-COase-like_fold.
IPR006478. Formate_DH_asu.
IPR006656. Mopterin_OxRdtase.
IPR006963. Mopterin_OxRdtase_Fe4S4.
IPR006655. Mopterin_OxRdtase_prok_CS.
IPR006657. MPT_dinuc_bd.
[Graphical view]

Gene3D

G3DSA:2.40.40.20. Asp_decarboxylase-like_fold. 1 hit.

Pfam

PF04879. Molybdop_Fe4S4. 1 hit.
PF00384. Molybdopterin. 1 hit.
PF01568. Molydop_binding. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01591. Fdh-alpha. 1 hit.

PROSITE

PS00551. MOLYBDOPTERIN_PROK_1. 1 hit.
PS00490. MOLYBDOPTERIN_PROK_2. 1 hit.
PS00932. MOLYBDOPTERIN_PROK_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

FDHF_ECOLI

Accession

Primary (citable) accession number: P07658
Secondary accession number(s): P78137, Q2M6M5

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	February 26, 2008
Last modified:	November 3, 2009
This is version 111 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)