>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD; InterPro: IPR014138 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are related families..

Probab=94.49  E-value=0.25  Score=29.53  Aligned_cols=132  Identities=17%  Similarity=0.259  Sum_probs=71.9

Q ss_pred             HHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEE----------------------------
Q ss_conf             4167726776213100276999999999985101112333332124797589----------------------------
Q gi|254780332|r  215 GLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVG----------------------------  266 (504)
Q Consensus       215 Gl~~G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl----------------------------  266 (504)
T Consensus         8 ~lk~G~~~aLvG~SGSGKS~tc~A~Lg~L~---~~~~~-~~G~i~l~G~~~~~~p~kemr~~Rg~~~~~imQnPr~AFNP   83 (239)
T TIGR02770         8 SLKRGEVLALVGESGSGKSLTCLAILGLLP---PGLTQ-TSGEILLDGRPLLALPKKEMRSIRGRHIATIMQNPRTAFNP   83 (239)
T ss_pred             EEECCEEEEEECCCCCCHHHHHHHHHCCCC---CCCEE-EEEEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             033243788874878758999999850358---65223-10266771723145873689988666630110285000016


Q ss_pred             -----------EEECCCCH-HHHHHHHHHHHHHHCCC---CCCC---CCCCHHHHHHHHHHHHHHHHCCEEEECCCCCCH
Q ss_conf             -----------99585217-99987899998741011---0001---213768899899999998627807825899889
Q gi|254780332|r  267 -----------FYSLEMSS-EQLATRIISEQTEVPSS---KIRR---GELTRPDYEKIVACSQVMQKLPLYIDQTGGISM  328 (504)
Q Consensus       267 -----------~fSlEMs~-~el~~R~is~~s~I~~~---~i~~---g~l~~~e~~~i~~a~~~l~~~~l~I~d~~~~ti  328 (504)
T Consensus        84 l~tm~~h~~ETl~~~~k~~k~~A~~~~~~~l~~VgL~~~~~~L~~YPF~LSGGMLQRvMIAlA~~~~~PfLiADEPTTdL  163 (239)
T TIGR02770        84 LLTMAEHAIETLRSLGKLSKKQARALILEALEAVGLEDPEEVLKKYPFQLSGGMLQRVMIALALLLEPPFLIADEPTTDL  163 (239)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCEECCCCCCHH
T ss_conf             76399999999997217461017999999998638522799997466413686278999999998557101417998387


Q ss_pred             H-----HHHHHHHHHCCCCCCCEEEEC
Q ss_conf             9-----999988640224447467767
Q gi|254780332|r  329 S-----QLATRARRLKRQRGLDLLIVD  350 (504)
Q Consensus       329 ~-----~I~~~~r~~~~~~gi~~vvID  350 (504)
T Consensus       164 Dv~~Q~~vL~~L~~l~~~~G~giLLiT  190 (239)
T TIGR02770       164 DVVVQARVLKLLDELRQKRGTGILLIT  190 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCEEEEEE
T ss_conf             799999999999999875187226520