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Formate dehydrogenase H (EC 1.17.1.9) (EC 1.17.99.7) (Formate dehydrogenase-H subunit alpha) (FDH-H) (Formate-hydrogen-lyase-linked, selenocysteine-containing polypeptide)

 FDHF_ECOLI              Reviewed;         715 AA.
P07658; P78137; Q2M6M5;
01-APR-1988, integrated into UniProtKB/Swiss-Prot.
26-FEB-2008, sequence version 2.
20-JUN-2018, entry version 186.
RecName: Full=Formate dehydrogenase H;
EC=1.17.1.9 {ECO:0000269|PubMed:16830149, ECO:0000269|PubMed:9036855, ECO:0000269|PubMed:9521673};
EC=1.17.99.7 {ECO:0000269|PubMed:16830149, ECO:0000269|PubMed:9036855, ECO:0000269|PubMed:9521673};
AltName: Full=Formate dehydrogenase-H subunit alpha;
Short=FDH-H;
AltName: Full=Formate-hydrogen-lyase-linked, selenocysteine-containing polypeptide;
Name=fdhF; OrderedLocusNames=b4079, JW4040;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
PubMed=2941757; DOI=10.1073/pnas.83.13.4650;
Zinoni F., Birkmann A., Stadtman T.C., Boeck A.;
"Nucleotide sequence and expression of the selenocysteine-containing
polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked)
from Escherichia coli.";
Proc. Natl. Acad. Sci. U.S.A. 83:4650-4654(1986).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=8265357; DOI=10.1093/nar/21.23.5408;
Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J.,
Daniels D.L.;
"Analysis of the Escherichia coli genome. IV. DNA sequence of the
region from 89.2 to 92.8 minutes.";
Nucleic Acids Res. 21:5408-5417(1993).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
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.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[5]
PROTEIN SEQUENCE OF 1-12, AND CHARACTERIZATION.
PubMed=2211698;
Axley M.J., Grahame D.A., Stadtman T.C.;
"Escherichia coli formate-hydrogen lyase. Purification and properties
of the selenium-dependent formate dehydrogenase component.";
J. Biol. Chem. 265:18213-18218(1990).
[6]
ENZYME REGULATION, AND CRYSTALLIZATION.
PubMed=8626495; DOI=10.1074/jbc.271.14.8095;
Gladyshev V.N., Boyington J.C., Khangulov S.V., Grahame D.A.,
Stadtman T.C., Sun P.D.;
"Characterization of crystalline formate dehydrogenase H from
Escherichia coli. Stabilization, EPR spectroscopy, and preliminary
crystallographic analysis.";
J. Biol. Chem. 271:8095-8100(1996).
[7]
CATALYTIC ACTIVITY, ENZYME REGULATION, AND COFACTOR.
PubMed=9521673; DOI=10.1021/bi972177k;
Khangulov S.V., Gladyshev V.N., Dismukes G.C., Stadtman T.C.;
"Selenium-containing formate dehydrogenase H from Escherichia coli: a
molybdopterin enzyme that catalyzes formate oxidation without oxygen
transfer.";
Biochemistry 37:3518-3528(1998).
[8]
X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
(4FE-4S); MOLYBDENUM ION AND MOLYBDOPTERIN, SELENOCYSTEINE AT SEC-140,
COFACTOR, AND CATALYTIC ACTIVITY.
PubMed=9036855; DOI=10.1126/science.275.5304.1305;
Boyington J.C., Gladyshev V.N., Khangulov S.V., Stadtman T.C.,
Sun P.D.;
"Crystal structure of formate dehydrogenase H: catalysis involving Mo,
molybdopterin, selenocysteine, and an Fe4S4 cluster.";
Science 275:1305-1308(1997).
[9]
X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS) IN COMPLEX WITH IRON-SULFUR
(4FE-4S) AND MOLYBDOPTERIN, AND CATALYTIC ACTIVITY.
PubMed=16830149; DOI=10.1007/s00775-006-0129-2;
Raaijmakers H.C., Romao M.J.;
"Formate-reduced E. coli formate dehydrogenase H: The reinterpretation
of the crystal structure suggests a new reaction mechanism.";
J. Biol. Inorg. Chem. 11:849-854(2006).
-!- FUNCTION: Decomposes formic acid to hydrogen and carbon dioxide
under anaerobic conditions in the absence of exogenous electron
acceptors.
-!- CATALYTIC ACTIVITY: Formate + NAD(+) = CO(2) + NADH.
{ECO:0000269|PubMed:16830149, ECO:0000269|PubMed:9036855,
ECO:0000269|PubMed:9521673}.
-!- CATALYTIC ACTIVITY: Formate + acceptor = CO(2) + reduced acceptor.
{ECO:0000269|PubMed:16830149, ECO:0000269|PubMed:9036855,
ECO:0000269|PubMed:9521673}.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Note=Binds 1 [4Fe-4S] cluster per subunit.;
-!- COFACTOR:
Name=Mo-bis(molybdopterin guanine dinucleotide);
Xref=ChEBI:CHEBI:60539;
Note=Binds 1 molybdenum-bis(molybdopterin guanine dinucleotide)
(Mo-bis-MGD) cofactor per subunit.;
-!- ENZYME REGULATION: Inhibited by aerobic conditions.
{ECO:0000269|PubMed:8626495, ECO:0000269|PubMed:9521673}.
-!- SUBUNIT: Consists of two separable enzymatic activities: a formate
dehydrogenase component (FDH-H) and hydrogenase-3.
{ECO:0000269|PubMed:16830149, ECO:0000269|PubMed:9036855}.
-!- INTERACTION:
P16433:hycG; NbExp=3; IntAct=EBI-1121603, EBI-541977;
-!- INDUCTION: By formate. Repressed by oxygen, nitrate, nitrite, and
other electron acceptors.
-!- SIMILARITY: Belongs to the prokaryotic molybdopterin-containing
oxidoreductase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; M13563; AAA23754.2; -; Genomic_DNA.
EMBL; U00006; AAC43173.2; -; Genomic_DNA.
EMBL; U00096; AAD13462.1; -; Genomic_DNA.
EMBL; AP009048; BAE78081.1; -; Genomic_DNA.
PIR; A24145; DEECFS.
RefSeq; NP_418503.1; NC_000913.3.
RefSeq; WP_001300547.1; NZ_LN832404.1.
PDB; 1AA6; X-ray; 2.30 A; A=1-715.
PDB; 1FDI; X-ray; 2.90 A; A=1-715.
PDB; 1FDO; X-ray; 2.80 A; A=1-715.
PDB; 2IV2; X-ray; 2.27 A; X=1-715.
PDBsum; 1AA6; -.
PDBsum; 1FDI; -.
PDBsum; 1FDO; -.
PDBsum; 2IV2; -.
ProteinModelPortal; P07658; -.
SMR; P07658; -.
BioGrid; 4262950; 28.
ComplexPortal; CPX-317; Formate hydrogenlyase-H/Hydrogenase-3 complex.
DIP; DIP-9572N; -.
IntAct; P07658; 13.
STRING; 316385.ECDH10B_4270; -.
DrugBank; DB02345; Selenocysteine.
TCDB; 3.D.1.9.2; the h(+) or na(+)-translocating nadh dehydrogenase (ndh) family.
PaxDb; P07658; -.
PRIDE; P07658; -.
EnsemblBacteria; AAD13462; AAD13462; b4079.
EnsemblBacteria; BAE78081; BAE78081; BAE78081.
GeneID; 948584; -.
KEGG; ecj:JW4040; -.
KEGG; eco:b4079; -.
PATRIC; fig|511145.12.peg.4203; -.
EchoBASE; EB0281; -.
EcoGene; EG10285; fdhF.
eggNOG; ENOG4107QIW; Bacteria.
eggNOG; COG0243; LUCA.
HOGENOM; HOG000031440; -.
InParanoid; P07658; -.
KO; K22015; -.
OMA; AWPEKTG; -.
PhylomeDB; P07658; -.
BioCyc; EcoCyc:FORMATEDEHYDROGH-MONOMER; -.
BioCyc; MetaCyc:FORMATEDEHYDROGH-MONOMER; -.
BRENDA; 1.1.99.33; 2026.
BRENDA; 1.2.1.2; 2026.
EvolutionaryTrace; P07658; -.
PRO; PR:P07658; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
GO; GO:0009055; F:electron transfer activity; IEA:InterPro.
GO; GO:0008863; F:formate dehydrogenase (NAD+) activity; IEA:InterPro.
GO; GO:0030151; F:molybdenum ion binding; IDA:EcoCyc.
GO; GO:0043546; F:molybdopterin cofactor binding; IEA:InterPro.
GO; GO:0003954; F:NADH dehydrogenase activity; IBA:GO_Central.
GO; GO:0015944; P:formate oxidation; IDA:EcoCyc.
InterPro; IPR009010; Asp_de-COase-like_dom_sf.
InterPro; IPR006478; Formate_DH_asu.
InterPro; IPR006657; MoPterin_dinucl-bd_dom.
InterPro; IPR006656; Mopterin_OxRdtase.
InterPro; IPR006963; Mopterin_OxRdtase_4Fe-4S_dom.
InterPro; IPR006655; Mopterin_OxRdtase_prok_CS.
InterPro; IPR027467; MopterinOxRdtase_cofactor_BS.
Pfam; PF04879; Molybdop_Fe4S4; 1.
Pfam; PF00384; Molybdopterin; 1.
Pfam; PF01568; Molydop_binding; 1.
SMART; SM00926; Molybdop_Fe4S4; 1.
SUPFAM; SSF50692; SSF50692; 1.
TIGRFAMs; TIGR01591; Fdh-alpha; 1.
PROSITE; PS51669; 4FE4S_MOW_BIS_MGD; 1.
PROSITE; PS00551; MOLYBDOPTERIN_PROK_1; 1.
PROSITE; PS00490; MOLYBDOPTERIN_PROK_2; 1.
PROSITE; PS00932; MOLYBDOPTERIN_PROK_3; 1.
1: Evidence at protein level;
3D-structure; 4Fe-4S; Complete proteome; Direct protein sequencing;
Iron; Iron-sulfur; Metal-binding; Molybdenum; NAD; Oxidoreductase;
Reference proteome; Selenocysteine.
CHAIN 1 715 Formate dehydrogenase H.
/FTId=PRO_0000063221.
DOMAIN 1 56 4Fe-4S Mo/W bis-MGD-type.
{ECO:0000255|PROSITE-ProRule:PRU01004}.
REGION 110 112 MGD 1 binding.
REGION 173 180 MGD 2 binding.
REGION 201 204 MGD 2 binding.
REGION 221 223 MGD 2 binding.
REGION 402 410 MGD 1 binding.
REGION 428 429 MGD 1 binding.
REGION 579 581 MGD 1 binding.
REGION 581 587 MGD 2 binding.
REGION 661 662 MGD 1 binding.
ACT_SITE 44 44 Electron donor/acceptor.
ACT_SITE 140 140 Proton donor/acceptor.
METAL 8 8 Iron-sulfur (4Fe-4S).
{ECO:0000255|PROSITE-ProRule:PRU01004,
ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
METAL 10 10 Iron-sulfur (4Fe-4S).
{ECO:0000255|PROSITE-ProRule:PRU01004,
ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
METAL 11 11 Iron-sulfur (4Fe-4S).
{ECO:0000255|PROSITE-ProRule:PRU01004,
ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
METAL 15 15 Iron-sulfur (4Fe-4S).
{ECO:0000255|PROSITE-ProRule:PRU01004,
ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
METAL 42 42 Iron-sulfur (4Fe-4S).
{ECO:0000255|PROSITE-ProRule:PRU01004,
ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
METAL 140 140 Molybdenum.
BINDING 44 44 Molybdopterin guanine dinucleotide 2.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 297 297 Molybdopterin guanine dinucleotide 2; via
amide nitrogen.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 301 301 Molybdopterin guanine dinucleotide 1.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 335 335 Molybdopterin guanine dinucleotide 1.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 445 445 Molybdopterin guanine dinucleotide 1.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 478 478 Molybdopterin guanine dinucleotide 1.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 588 588 Molybdopterin guanine dinucleotide 1; via
amide nitrogen.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 654 654 Molybdopterin guanine dinucleotide 1.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 655 655 Molybdopterin guanine dinucleotide 2.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 678 678 Molybdopterin guanine dinucleotide 1.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
BINDING 679 679 Molybdopterin guanine dinucleotide 2.
{ECO:0000269|PubMed:16830149,
ECO:0000269|PubMed:9036855}.
SITE 141 141 Important for catalytic activity.
SITE 333 333 Important for catalytic activity.
NON_STD 140 140 Selenocysteine.
{ECO:0000269|PubMed:9036855}.
CONFLICT 19 19 L -> V (in Ref. 1; AAA23754).
{ECO:0000305}.
STRAND 2 7 {ECO:0000244|PDB:2IV2}.
STRAND 9 11 {ECO:0000244|PDB:2IV2}.
STRAND 16 22 {ECO:0000244|PDB:2IV2}.
STRAND 25 31 {ECO:0000244|PDB:2IV2}.
TURN 35 39 {ECO:0000244|PDB:2IV2}.
HELIX 43 47 {ECO:0000244|PDB:2IV2}.
HELIX 50 53 {ECO:0000244|PDB:2IV2}.
STRAND 57 59 {ECO:0000244|PDB:2IV2}.
STRAND 69 72 {ECO:0000244|PDB:1AA6}.
HELIX 80 98 {ECO:0000244|PDB:2IV2}.
HELIX 100 102 {ECO:0000244|PDB:2IV2}.
STRAND 103 106 {ECO:0000244|PDB:2IV2}.
HELIX 114 126 {ECO:0000244|PDB:2IV2}.
HELIX 137 140 {ECO:0000244|PDB:1AA6}.
STRAND 143 145 {ECO:0000244|PDB:2IV2}.
HELIX 148 152 {ECO:0000244|PDB:2IV2}.
HELIX 161 166 {ECO:0000244|PDB:2IV2}.
STRAND 168 174 {ECO:0000244|PDB:2IV2}.
HELIX 177 180 {ECO:0000244|PDB:2IV2}.
HELIX 182 193 {ECO:0000244|PDB:2IV2}.
STRAND 197 201 {ECO:0000244|PDB:2IV2}.
HELIX 207 210 {ECO:0000244|PDB:2IV2}.
STRAND 213 216 {ECO:0000244|PDB:2IV2}.
HELIX 223 236 {ECO:0000244|PDB:2IV2}.
HELIX 242 248 {ECO:0000244|PDB:2IV2}.
HELIX 252 260 {ECO:0000244|PDB:2IV2}.
HELIX 265 267 {ECO:0000244|PDB:2IV2}.
HELIX 268 271 {ECO:0000244|PDB:2IV2}.
HELIX 275 287 {ECO:0000244|PDB:2IV2}.
STRAND 288 296 {ECO:0000244|PDB:2IV2}.
HELIX 299 301 {ECO:0000244|PDB:2IV2}.
STRAND 302 304 {ECO:0000244|PDB:2IV2}.
HELIX 305 318 {ECO:0000244|PDB:2IV2}.
STRAND 322 324 {ECO:0000244|PDB:2IV2}.
STRAND 328 332 {ECO:0000244|PDB:2IV2}.
HELIX 338 343 {ECO:0000244|PDB:2IV2}.
HELIX 352 354 {ECO:0000244|PDB:2IV2}.
HELIX 360 369 {ECO:0000244|PDB:2IV2}.
HELIX 383 385 {ECO:0000244|PDB:2IV2}.
HELIX 386 391 {ECO:0000244|PDB:2IV2}.
STRAND 397 402 {ECO:0000244|PDB:2IV2}.
HELIX 405 408 {ECO:0000244|PDB:2IV2}.
STRAND 409 411 {ECO:0000244|PDB:2IV2}.
HELIX 412 421 {ECO:0000244|PDB:2IV2}.
STRAND 422 431 {ECO:0000244|PDB:2IV2}.
HELIX 434 437 {ECO:0000244|PDB:2IV2}.
STRAND 440 445 {ECO:0000244|PDB:2IV2}.
HELIX 448 450 {ECO:0000244|PDB:1AA6}.
STRAND 453 456 {ECO:0000244|PDB:2IV2}.
STRAND 460 465 {ECO:0000244|PDB:2IV2}.
STRAND 472 474 {ECO:0000244|PDB:2IV2}.
HELIX 478 488 {ECO:0000244|PDB:2IV2}.
HELIX 498 508 {ECO:0000244|PDB:2IV2}.
TURN 510 514 {ECO:0000244|PDB:2IV2}.
HELIX 517 520 {ECO:0000244|PDB:2IV2}.
TURN 521 523 {ECO:0000244|PDB:2IV2}.
STRAND 526 528 {ECO:0000244|PDB:2IV2}.
STRAND 541 543 {ECO:0000244|PDB:2IV2}.
STRAND 553 556 {ECO:0000244|PDB:1FDI}.
STRAND 571 573 {ECO:0000244|PDB:2IV2}.
STRAND 575 579 {ECO:0000244|PDB:2IV2}.
STRAND 583 585 {ECO:0000244|PDB:1FDI}.
HELIX 592 594 {ECO:0000244|PDB:2IV2}.
HELIX 596 599 {ECO:0000244|PDB:2IV2}.
STRAND 607 611 {ECO:0000244|PDB:2IV2}.
HELIX 612 618 {ECO:0000244|PDB:2IV2}.
STRAND 625 629 {ECO:0000244|PDB:2IV2}.
STRAND 634 645 {ECO:0000244|PDB:2IV2}.
STRAND 649 652 {ECO:0000244|PDB:2IV2}.
STRAND 657 659 {ECO:0000244|PDB:1FDI}.
HELIX 661 663 {ECO:0000244|PDB:1FDO}.
TURN 671 673 {ECO:0000244|PDB:1FDO}.
STRAND 681 687 {ECO:0000244|PDB:2IV2}.
HELIX 691 713 {ECO:0000244|PDB:2IV2}.
SEQUENCE 715 AA; 79374 MW; C7C86F6F704A142D CRC64;
MKKVVTVCPY CASGCKINLV VDNGKIVRAE AAQGKTNQGT LCLKGYYGWD FINDTQILTP
RLKTPMIRRQ RGGKLEPVSW DEALNYVAER LSAIKEKYGP DAIQTTGSSR GTGNETNYVM
QKFARAVIGT NNVDCCARVU HGPSVAGLHQ SVGNGAMSNA INEIDNTDLV FVFGYNPADS
HPIVANHVIN AKRNGAKIIV CDPRKIETAR IADMHIALKN GSNIALLNAM GHVIIEENLY
DKAFVASRTE GFEEYRKIVE GYTPESVEDI TGVSASEIRQ AARMYAQAKS AAILWGMGVT
QFYQGVETVR SLTSLAMLTG NLGKPHAGVN PVRGQNNVQG ACDMGALPDT YPGYQYVKDP
ANREKFAKAW GVESLPAHTG YRISELPHRA AHGEVRAAYI MGEDPLQTDA ELSAVRKAFE
DLELVIVQDI FMTKTASAAD VILPSTSWGE HEGVFTAADR GFQRFFKAVE PKWDLKTDWQ
IISEIATRMG YPMHYNNTQE IWDELRHLCP DFYGATYEKM GELGFIQWPC RDTSDADQGT
SYLFKEKFDT PNGLAQFFTC DWVAPIDKLT DEYPMVLSTV REVGHYSCRS MTGNCAALAA
LADEPGYAQI NTEDAKRLGI EDEALVWVHS RKGKIITRAQ VSDRPNKGAI YMTYQWWIGA
CNELVTENLS PITKTPEYKY CAVRVEPIAD QRAAEQYVID EYNKLKTRLR EAALA


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