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PDBsum entry 1kqf

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1kqf
Jmol
Contents
Protein chains
982 a.a. *
289 a.a. *
216 a.a. *
Ligands
SF4 ×5
MGD ×2
HEM ×2
CDL
Metals
6MO
Waters ×1989
* Residue conservation analysis
PDB id:
1kqf
Name: Oxidoreductase
Title: Formate dehydrogenase n from e. Coli
Structure: Formate dehydrogenase, nitrate-inducible, major s chain: a. Synonym: formate dehydrogenase-n alpha subunit. Fdh-n alpha anaerobic formate dehydrogenase major subunit. Other_details: native (oxidized) structure. Formate dehydrogenase, nitrate-inducible, iron-su subunit. Chain: b. Synonym: formate dehydrogenase-n beta subunit. Fdh-n beta s
Source: Escherichia coli. Organism_taxid: 562. Strain: gl101. Strain: gl101
Biol. unit: Nonamer (from PDB file)
Resolution:
1.60Å     R-factor:   0.177     R-free:   0.195
Authors: M.Jormakka,S.Tornroth,B.Byrne,S.Iwata
Key ref:
M.Jormakka et al. (2002). Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science, 295, 1863-1868. PubMed id: 11884747 DOI: 10.1126/science.1068186
Date:
05-Jan-02     Release date:   15-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24183  (FDNG_ECOLI) -  Formate dehydrogenase, nitrate-inducible, major subunit
Seq:
Struc:
 
Seq:
Struc:
1015 a.a.
982 a.a.*
Protein chain
Pfam   ArchSchema ?
P0AAJ3  (FDNH_ECOLI) -  Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit
Seq:
Struc:
294 a.a.
289 a.a.
Protein chain
Pfam   ArchSchema ?
P0AEK7  (FDNI_ECOLI) -  Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit
Seq:
Struc:
217 a.a.
216 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.1.1.5.6  - Formate dehydrogenase-N.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Formate + a quinone = CO2 + a quinol
Formate
+ quinone
= CO(2)
+ quinol
      Cofactor: Heme; Iron-sulfur; Molybdopterin guanine dinucleotide
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Iron-sulfur
Molybdopterin guanine dinucleotide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     electron carrier activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1126/science.1068186 Science 295:1863-1868 (2002)
PubMed id: 11884747  
 
 
Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.
M.Jormakka, S.Törnroth, B.Byrne, S.Iwata.
 
  ABSTRACT  
 
The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 angstroms through the enzyme. The menaquinone reduction site associated with a possible proton pathway was also characterized. This structure provides critical insights into the proton motive force generation by redox loop, a common mechanism among a wide range of respiratory enzymes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. A proposal for how proton motive force is generated by Fdh-N and nitrate reductase in Escherichia coli inner membrane. MK, menaquinone; MKH[2], reduced form of menaquinone; MGD, molybdopterin-guanine dinucleotide; b, heme b; FeS, iron-sulfur cluster.
Figure 2.
Fig. 2. Overall structure of Fdh-N. The figures are based on the native Fdh-N structure except for the position of HQNO, which is determined in the Fdh-N and HQNO complex structure. The , , and subunits are shown in brown, blue, and magenta, respectively. Heme groups and MGD cofactors are shown in green, and Mo, cardiolipin (CL), and HQNO are colored in magenta, yellow, and navy, respectively. Five [4Fe-4S] clusters are painted as red (Fe atoms) and yellow (S atoms). (A) Fdh-N trimer viewed parallel to the membrane. (B) Fdh-N trimer viewed from the periplasm along the membrane normal. (C) View of the Fdh-N monomer parallel to the membrane. Center-to-center and edge-to-edge (in parentheses) (12) distances in angstroms between each of the redox centers are also shown. The edge-to-edge distance for HQNO to heme b[C] is 0 because HQNO is directly binding to the histidine ligand of heme b[C]. All figures were made with MOLSCRIPT (28) and BOBSCRIPT (29) and rendered with RASTER3D (30).
 
  The above figures are reprinted by permission from the AAAs: Science (2002, 295, 1863-1868) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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The twin-arginine translocation (Tat) protein export pathway.
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20819103 X.Zhang, E.G.Matson, and J.R.Leadbetter (2011).
Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood-feeding termites and a wood-feeding roach.
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20645325 E.Cremades, J.Echeverría, and S.Alvarez (2010).
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Structures of membrane proteins.
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The role of phosphatidic acid and cardiolipin in stability of the tetrameric assembly of potassium channel KcsA.
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20406421 N.Borgese, and M.Righi (2010).
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20587053 T.E.Meyer, J.A.Kyndt, and M.A.Cusanovich (2010).
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19371718 E.Mileykovskaya, and W.Dowhan (2009).
Cardiolipin membrane domains in prokaryotes and eukaryotes.
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19536822 G.Zoppellaro, K.L.Bren, A.A.Ensign, E.Harbitz, R.Kaur, H.P.Hersleth, U.Ryde, L.Hederstedt, and K.K.Andersson (2009).
Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination.
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Molybdenum and tungsten enzymes: a crystallographic and mechanistic overview.
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19206188 S.Groysman, and R.H.Holm (2009).
Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites.
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19233927 X.Li, Q.Luo, N.Q.Wofford, K.L.Keller, M.J.McInerney, J.D.Wall, and L.R.Krumholz (2009).
A molybdopterin oxidoreductase is involved in H2 oxidation in Desulfovibrio desulfuricans G20.
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18658261 B.S.Pickering, and I.J.Oresnik (2008).
Formate-dependent autotrophic growth in Sinorhizobium meliloti.
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18615097 C.F.Matos, C.Robinson, and A.Di Cola (2008).
The Tat system proofreads FeS protein substrates and directly initiates the disposal of rejected molecules.
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18247347 C.H.Lu, S.W.Huang, Y.L.Lai, C.P.Lin, C.H.Shih, C.C.Huang, W.L.Hsu, and J.K.Hwang (2008).
On the relationship between the protein structure and protein dynamics.
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18418633 E.A.Berry, and F.A.Walker (2008).
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18535145 G.J.Workun, K.Moquin, R.A.Rothery, and J.H.Weiner (2008).
Evolutionary persistence of the molybdopyranopterin-containing sulfite oxidase protein fold.
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18716757 I.Lüke, G.Butland, K.Moore, G.Buchanan, V.Lyall, S.A.Fairhurst, J.F.Greenblatt, A.Emili, T.Palmer, and F.Sargent (2008).
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Lipids in the assembly of membrane proteins and organization of protein supercomplexes: implications for lipid-linked disorders.
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18536726 M.Jormakka, K.Yokoyama, T.Yano, M.Tamakoshi, S.Akimoto, T.Shimamura, P.Curmi, and S.Iwata (2008).
Molecular mechanism of energy conservation in polysulfide respiration.
  Nat Struct Mol Biol, 15, 730-737.
PDB codes: 2vpw 2vpx 2vpy 2vpz
18077827 M.Schlame (2008).
Cardiolipin synthesis for the assembly of bacterial and mitochondrial membranes.
  J Lipid Res, 49, 1607-1620.  
18500332 N.H.Joh, A.Min, S.Faham, J.P.Whitelegge, D.Yang, V.L.Woods, and J.U.Bowie (2008).
Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins.
  Nature, 453, 1266-1270.
PDB codes: 3coc 3cod
18218713 S.Newstead, S.Ferrandon, and S.Iwata (2008).
Rationalizing alpha-helical membrane protein crystallization.
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18667702 T.Reda, C.M.Plugge, N.J.Abram, and J.Hirst (2008).
Reversible interconversion of carbon dioxide and formate by an electroactive enzyme.
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18501187 W.Liu, C.E.Rogge, G.F.da Silva, V.P.Shinkarev, A.L.Tsai, Y.Kamensky, G.Palmer, and R.J.Kulmacz (2008).
His92 and His110 selectively affect different heme centers of adrenal cytochrome b(561).
  Biochim Biophys Acta, 1777, 1218-1228.  
17600788 K.Pal, P.K.Chaudhury, and S.Sarkar (2007).
Structure of the Michaelis complex and function of the catalytic center in the reductive half-reaction of computational and synthetic models of sulfite oxidase.
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17557793 N.Buzhynskyy, P.Sens, V.Prima, J.N.Sturgis, and S.Scheuring (2007).
Rows of ATP synthase dimers in native mitochondrial inner membranes.
  Biophys J, 93, 2870-2876.  
16962969 D.P.Kloer, C.Hagel, J.Heider, and G.E.Schulz (2006).
Crystal structure of ethylbenzene dehydrogenase from Aromatoleum aromaticum.
  Structure, 14, 1377-1388.
PDB code: 2ivf
16830149 H.C.Raaijmakers, and M.J.Romão (2006).
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.
PDB code: 2iv2
16885262 H.Ridley, C.A.Watts, D.J.Richardson, and C.S.Butler (2006).
Resolution of distinct membrane-bound enzymes from Enterobacter cloacae SLD1a-1 that are responsible for selective reduction of nitrate and selenate oxyanions.
  Appl Environ Microbiol, 72, 5173-5180.  
17024183 M.G.Madej, H.R.Nasiri, N.S.Hilgendorff, H.Schwalbe, and C.R.Lancaster (2006).
Evidence for transmembrane proton transfer in a dihaem-containing membrane protein complex.
  EMBO J, 25, 4963-4970.
PDB code: 2bs2
16802174 M.John, R.P.Schmitz, M.Westermann, W.Richter, and G.Diekert (2006).
Growth substrate dependent localization of tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans.
  Arch Microbiol, 186, 99.  
17139260 M.L.Rodrigues, T.F.Oliveira, I.A.Pereira, and M.Archer (2006).
X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase NrfH reveals novel haem coordination.
  EMBO J, 25, 5951-5960.
PDB code: 2j7a
16597999 S.S.Ruebush, S.L.Brantley, and M.Tien (2006).
Reduction of soluble and insoluble iron forms by membrane fractions of Shewanella oneidensis grown under aerobic and anaerobic conditions.
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16433558 T.Teschner, L.Yatsunyk, V.Schünemann, H.Paulsen, H.Winkler, C.Hu, W.R.Scheidt, F.A.Walker, and A.X.Trautwein (2006).
Models of the membrane-bound cytochromes: mössbauer spectra of crystalline low-spin ferriheme complexes having axial ligand plane dihedral angles ranging from 0 degree to 90 degrees.
  J Am Chem Soc, 128, 1379-1389.  
16172928 A.J.Watson, A.V.Hughes, P.K.Fyfe, M.C.Wakeham, K.Holden-Dye, P.Heathcote, and M.R.Jones (2005).
On the role of basic residues in adapting the reaction centre-LH1 complex for growth at elevated temperatures in purple bacteria.
  Photosynth Res, 86, 81.  
15802249 B.C.Berks, T.Palmer, and F.Sargent (2005).
Protein targeting by the bacterial twin-arginine translocation (Tat) pathway.
  Curr Opin Microbiol, 8, 174-181.  
16380425 C.R.Lancaster, U.S.Sauer, R.Gross, A.H.Haas, J.Graf, H.Schwalbe, W.Mäntele, J.Simon, and M.G.Madej (2005).
Experimental support for the "E pathway hypothesis" of coupled transmembrane e- and H+ transfer in dihemic quinol:fumarate reductase.
  Proc Natl Acad Sci U S A, 102, 18860-18865.
PDB codes: 2bs3 2bs4
15819632 M.L.Crouch, L.A.Becker, I.S.Bang, H.Tanabe, A.J.Ouellette, and F.C.Fang (2005).
The alternative sigma factor sigma is required for resistance of Salmonella enterica serovar Typhimurium to anti-microbial peptides.
  Mol Microbiol, 56, 789-799.  
15949761 P.K.Fyfe, A.V.Hughes, P.Heathcote, and M.R.Jones (2005).
Proteins, chlorophylls and lipids: X-ray analysis of a three-way relationship.
  Trends Plant Sci, 10, 275-282.  
15654871 R.A.Rothery, A.M.Seime, A.M.Spiers, E.Maklashina, I.Schröder, R.P.Gunsalus, G.Cecchini, and J.H.Weiner (2005).
Defining the Q-site of Escherichia coli fumarate reductase by site-directed mutagenesis, fluorescence quench titrations and EPR spectroscopy.
  FEBS J, 272, 313-326.  
14681400 A.Andreeva, D.Howorth, S.E.Brenner, T.J.Hubbard, C.Chothia, and A.G.Murzin (2004).
SCOP database in 2004: refinements integrate structure and sequence family data.
  Nucleic Acids Res, 32, D226-D229.  
15516557 A.C.Fisher, and M.P.DeLisa (2004).
A little help from my friends: quality control of presecretory proteins in bacteria.
  J Bacteriol, 186, 7467-7473.  
15284442 A.Messerschmidt, H.Niessen, D.Abt, O.Einsle, B.Schink, and P.M.Kroneck (2004).
Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols.
  Proc Natl Acad Sci U S A, 101, 11571-11576.
PDB codes: 1ti2 1ti4 1ti6 1vld 1vle 1vlf
15342602 C.Punginelli, B.Ize, N.R.Stanley, V.Stewart, G.Sawers, B.C.Berks, and T.Palmer (2004).
mRNA secondary structure modulates translation of Tat-dependent formate dehydrogenase N.
  J Bacteriol, 186, 6311-6315.  
15028701 F.Peters, M.Rother, and M.Boll (2004).
Selenocysteine-containing proteins in anaerobic benzoate metabolism of Desulfococcus multivorans.
  J Bacteriol, 186, 2156-2163.  
15311335 J.J.Moura, C.D.Brondino, J.Trincão, and M.J.Romão (2004).
Mo and W bis-MGD enzymes: nitrate reductases and formate dehydrogenases.
  J Biol Inorg Chem, 9, 791-799.  
15551861 O.Einsle, and P.M.Kroneck (2004).
Structural basis of denitrification.
  Biol Chem, 385, 875-883.  
15321667 R.P.Schmitz, and G.Diekert (2004).
The fdh operon of Sulfurospirillum multivorans.
  FEMS Microbiol Lett, 237, 235-242.  
15498942 T.J.Stevens, K.Mizuguchi, and I.T.Arkin (2004).
Distinct protein interfaces in transmembrane domains suggest an in vivo folding model.
  Protein Sci, 13, 3028-3037.  
15486691 T.Tomiki, and N.Saitou (2004).
Phylogenetic analysis of proteins associated in the four major energy metabolism systems: photosynthesis, aerobic respiration, denitrification, and sulfur respiration.
  J Mol Evol, 59, 158-176.  
12594934 F.Baymann, E.Lebrun, M.Brugna, B.Schoepp-Cothenet, M.T.Giudici-Orticoni, and W.Nitschke (2003).
The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes.
  Philos Trans R Soc Lond B Biol Sci, 358, 267-274.  
12823811 J.Simon, M.Sänger, S.C.Schuster, and R.Gross (2003).
Electron transport to periplasmic nitrate reductase (NapA) of Wolinella succinogenes is independent of a NapC protein.
  Mol Microbiol, 49, 69-79.  
12940994 K.Hatzixanthis, T.Palmer, and F.Sargent (2003).
A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase.
  Mol Microbiol, 49, 1377-1390.  
14511372 M.G.Almeida, S.Macieira, L.L.Gonçalves, R.Huber, C.A.Cunha, M.J.Romão, C.Costa, J.Lampreia, J.J.Moura, and I.Moura (2003).
The isolation and characterization of cytochrome c nitrite reductase subunits (NrfA and NrfH) from Desulfovibrio desulfuricans ATCC 27774. Re-evaluation of the spectroscopic data and redox properties.
  Eur J Biochem, 270, 3904-3915.  
12910261 M.G.Bertero, R.A.Rothery, M.Palak, C.Hou, D.Lim, F.Blasco, J.H.Weiner, and N.C.Strynadka (2003).
Insights into the respiratory electron transfer pathway from the structure of nitrate reductase A.
  Nat Struct Biol, 10, 681-687.
PDB code: 1q16
12948771 M.Jormakka, B.Byrne, and S.Iwata (2003).
Formate dehydrogenase--a versatile enzyme in changing environments.
  Curr Opin Struct Biol, 13, 418-423.  
12815340 M.Machius (2003).
Structural biology: a high-tech tool for biomedical research.
  Curr Opin Nephrol Hypertens, 12, 431-438.  
12948779 P.D.Barker (2003).
Designing redox metalloproteins from bottom-up and top-down perspectives.
  Curr Opin Struct Biol, 13, 490-499.  
14640690 Z.Zhao, R.A.Rothery, and J.H.Weiner (2003).
Effects of site-directed mutations on heme reduction in Escherichia coli nitrate reductase A by menaquinol: a stopped-flow study.
  Biochemistry, 42, 14225-14233.  
11959503 B.Byrne, and S.Iwata (2002).
Membrane protein complexes.
  Curr Opin Struct Biol, 12, 239-243.  
12220497 H.Raaijmakers, S.Macieira, J.M.Dias, S.Teixeira, S.Bursakov, R.Huber, J.J.Moura, I.Moura, and M.J.Romão (2002).
Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas.
  Structure, 10, 1261-1272.
PDB code: 1h0h
12165429 J.Simon (2002).
Enzymology and bioenergetics of respiratory nitrite ammonification.
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11952800 S.Biel, J.Simon, R.Gross, T.Ruiz, M.Ruitenberg, and A.Kröger (2002).
Reconstitution of coupled fumarate respiration in liposomes by incorporating the electron transport enzymes isolated from Wolinella succinogenes.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.