>TIGR00391 hydA hydrogenase (NiFe) small subunit (hydA); InterPro: IPR001821 Hydrogenases catalyse the reversible oxidation of molecular hydrogen and play a vital role in anaerobic metabolism. Metal-containing hydrogenases are subdivided into three classes: Fe ('iron only') hydrogenases; Ni-Fe hydrogenases; and Ni-Fe-Se hydrogenases . Hydrogen oxidation is coupled to the reduction of electron acceptors (such as oxygen, nitrate, sulphate, carbon dioxide and fumarate), whereas proton reduction (hydrogen evolution) is essential in pyruvate fermentation or in the disposal of excess electrons. The Ni-Fe hydrogenases, when isolated, are found to catalyse both hydrogen evolution and uptake, with low-potential multihaem cytochromes, such as cytochrome c3, acting as either electron donors or acceptors, depending on their oxidation state . Both periplasmic (soluble) and membrane-bound hydrogenases are known. The Ni-Fe hydrogenases are heterodimeric proteins consisting of small (S) and large (L) subunits. The small subunit contains three iron-sulphur clusters (two [4Fe-4S] and one [3Fe-4S]); the large subunit contains a nickel ion , . Small subunits of membrane-bound Ni-Fe hydrogenases contain a C-terminal domain of about 40 residues that is absent in periplasmic forms. The 3D structure of the Ni-Fe hydrogenase from Desulfovibrio gigas has been determined at 2.85A resolution . The small subunit consists of two domains, I(S) and II(S). The alpha/beta twisted open sheet structure of the N-terminal I(S) domain is similar to that of flavodoxin; the C-terminal II(S) domain contains two alpha-helices and has no beta-structure. The Fe-S clusters are distributed almost along a straight line, with the [3Fe-4S] cluster located half-way between the two [4Fe-4S] clusters. The two [4Fe-4S] clusters have been termed proximal (prox) and distal (dist), based on their distance to the Ni atom. Domain I(S) binds the [4Fe-4S]prox cluster, while domain II(S) binds the [4Fe-4S]dist and [3Fe-4S] clusters. The [4Fe-4S]prox cluster is coordinated by Cys-17, Cys-20, Cys-112 and Cys-148; [4Fe-4S]dist is coordinated by His-185, Cys-188, Cys-213 and Cys-219; and [3Fe-4S] is coordinated by Cys-228, Cys-246 and Cys-249. [4Fe-4S]dist is the first known example of a [4Fe-4S] cluster in protein structure ligated by a His side chain. A crown of acidic residues surrounds the partially-exposed His-185 and this might provide a recognition site for the redox partner (cytochrome c3) . A mechanism of electron transfer from the Ni active site through the Fe-S clusters to the cytochrome c3 has been suggested . The role of the [3Fe-4S] cluster is not clear: its high redox potential and its absence from some homologous hydrogenases put its involvement in electron transfer in doubt .; GO: 0008901 ferredoxin hydrogenase activity, 0051536 iron-sulfur cluster binding, 0006118 electron transport, 0009375 ferredoxin hydrogenase complex.

Probab=95.94  E-value=0.012  Score=36.49  Aligned_cols=133  Identities=18%  Similarity=0.334  Sum_probs=79.6

Q ss_pred             EEEEHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCH------------------------------HHCC----E
Q ss_conf             88559999845612883477523546521356633666786------------------------------7648----4
Q gi|254780853|r   39 LVTSVDQLVTWARTGSLMWMTFGLACCAVEMMQASMPRYDL------------------------------ERFG----F   84 (185)
Q Consensus        39 i~t~~d~l~nW~R~~Slwp~~fg~aCC~iE~~a~~~p~yD~------------------------------eRfG----~   84 (185)
T Consensus        38 ~~~~~~~~~~~~~~p~~w~~~~~c~~c~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~  117 (370)
T TIGR00391        38 APLLAWAVENPPRLPVIWLHGLECTGCTESLLRSAHPTVEDLILDLISLEYHETLLAAAGFQAEENLHDALEKYKGKYIL  117 (370)
T ss_pred             HHHHHHHHHCCCCCCEEEEECHHHHHHHHHHHHHCCHHHHHHHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHCCCEEE
T ss_conf             46777764124557466730101100135665320303567777665200123444330202456677777752585689


Q ss_pred             EE-CCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCC--CCCEECCCCCCCCC--EEECCCC
Q ss_conf             87-0682206079971413455699999999846866619985355668863478--87220772223223--0674887
Q gi|254780853|r   85 AP-RASPRQSDVMIVAGTLTNKMASALRRVYDQMPEPRYVISMGSCANGGGYYHY--SYSVVRGCDRIVPV--DIYVPGC  159 (185)
Q Consensus        85 ~~-~~sPRqADvliVtG~vT~km~~~l~~~yeqmpePK~ViA~G~Ca~sGG~f~~--sY~v~~g~d~~iPV--DvyVPGC  159 (185)
T Consensus       118 ~~~g~~p~~~~~~~~~~p~~~---~~~~~~~~~~~~~~~~~~~g~c~~~g~~~~~~~~p~~~~~~~~~~~~~~~~~~pgc  194 (370)
T TIGR00391       118 AVEGGPPLGDEGLLCLGPSGE---PGVEELRKAAEGAAAIIAWGTCSSWGGVQAAGPNPTGATPLDKVLPDKPVINVPGC  194 (370)
T ss_pred             EECCCCCCCCCCEEEECCCCC---HHHHHHHHHHHHHHHEEEECCCCCCCCCCCCCCCCCCCCCHHHHCCCCCEEECCCC
T ss_conf             973877646550266336664---35788776542101001110100014310145674444312333167633434788


Q ss_pred             CCCHHHHHHHHHHHH
Q ss_conf             689899999999999
Q gi|254780853|r  160 PPTAEALIYGILLLQ  174 (185)
Q Consensus       160 PPrPeail~gl~~L~  174 (185)
T Consensus       195 pp~~~~~~~~~~~~~  209 (370)
T TIGR00391       195 PPNPDNLLATVLYLL  209 (370)
T ss_pred             CCCHHHHHHHHHHHH
T ss_conf             875025666666555