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		PDBsum entry 1kqg Go to PDB code: Oxidoreductase PDB id 1kqg Loading ... Contents Protein chains 982 a.a.* 289 a.a.* 216 a.a.* Ligands SF4 ×5 MGD ×2 CDL HEM ×2 HQO Metals 6MO Waters ×1984 * Residue conservation analysis PDB id: 1kqg Links PDBe RCSB MMDB JenaLib Proteopedia CATH SCOP PDBSWS PDBePISA CSA ProSAT Name: Oxidoreductase Title: Formate dehydrogenase n from e. Coli Structure: Formate dehydrogenase, nitrate-inducible, major subunit. Chain: a. Synonym: formate dehydrogenase-n alpha subunit. Fdh-n alpha subunit. Anaerobic formate dehydrogenase major subunit. Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit. Chain: b. Synonym: formate dehydrogenase-n beta subunit. Fdh-n beta subunit. Anaerobic formate dehydrogenase iron-sulfur subunit. Source: Escherichia coli. Organism_taxid: 562. Strain: gl101. Strain: gl101 Biol. unit: Nonamer (from PDB file) Resolution: 2.80Å R-factor: 0.198 R-free: 0.239 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 Headers References Protein chain ? P24183 (FDNG_ECOLI) - Formate dehydrogenase, nitrate-inducible, major subunit from Escherichia coli (strain K12) Seq:Struc: Seq:Struc: 1015 a.a. 982 a.a.* Protein chain ? P0AAJ3 (FDNH_ECOLI) - Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit from Escherichia coli (strain K12) Seq:Struc: 294 a.a. 289 a.a. Protein chain ? P0AEK7 (FDNI_ECOLI) - Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit from Escherichia coli (strain K12) 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 2: Chain A: E.C.1.17.5.3 - formate dehydrogenase-N. [IntEnz] [ExPASy] [KEGG] [BRENDA] Reaction: a quinone + formate + H+ = a quinol + CO2 quinone + formate + H(+) = quinol + CO2 Cofactor: Heme; Iron-sulfur; Molybdopterin guanine dinucleotide Heme Bound ligand (Het Group name = HEM) matches with 95.45% similarity Iron-sulfur Molybdopterin guanine dinucleotide Enzyme class 3: Chains B, C: E.C.1.2.1.2 - Transferred entry: 1.17.1.9. [IntEnz] [ExPASy] [KEGG] [BRENDA] Reaction: Formate + NAD+ = CO2 + NADH Formate + NAD(+) Bound ligand (Het Group name = MGD) matches with 75.00% similarity = CO(2) + NADH Cofactor: Flavin; Iron-sulfur; Mo cation Flavin Iron-sulfur Mo cation Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein. Molecule diagrams generated from .mol files obtained from theKEGG ftp site 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 22683878 T.Palmer, and B.C.Berks (2012). The twin-arginine translocation (Tat) protein export pathway. Nat Rev Microbiol,10, 483-496. 21289038 J.Speck, K.M.Arndt, and K.M.Müller (2011). Efficient phage display of intracellularly folded proteins mediated by the TAT pathway. Protein Eng Des Sel,24, 473-484. 20938980 K.Illergård, A.Kauko, and A.Elofsson (2011). 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