Clostridium active site

Selenocysteine was identified in 1976 (57) in a protein produced by Clostridium stricklandii, and it is thought to be the form in which selenium is incorporated, stoichiometricaHy, into proteins. Studies with rats show that over 80% of the dietary selenium given them is incorporated into proteins, thus selenocysteine takes on metaboHc importance. Selenoproteins having known enzymatic activities contain selenocysteine at the active sites. Two other forms of metabohc selenium are recognized methylated selenium compounds are synthesized for excretion, and selenium is incorporated into some transfer ribonucleic acids (tRNAs) in cultured cells (58). Some of the more important seleno-compounds are Hsted in Table 4. Examples of simple ring compounds are shown in Eigure 4. 

Figure 17 X-Ray structure of the active site of the rubredoxin from Clostridium pasteurianum...

Lemon, B. J. and Peters, J. W. (1999) Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum. Biochemistry, 38, 12969-73. 

The active site in Clostridium pasteurianum (Figure 8.1) contains a large unit characterized by an unusual arrangement of two moieties, an Fc4S4 iron protein... 

Enzyme preparations from Clostridium perfringens and Escherichia coli are commercially available, and the latter enzyme [69] has been cloned, overexpressed [70-72], and crystallized [73]. Its spatial structure has been determined recently by X-ray crystallography at 2.2 A resolution which has revealed that the enzyme is a tetramer and belongs to the a//l-barrel class of proteins [74] (Fig. 4). The active site pocket is located at the carboxy-terminal end of the eight-stranded /1-barrel, and the reactive lysine residue, forming a Schiff base with pyruvate, has been identified to be Lysl65 (Fig. 5). However, the current X-ray model excludes the catalytic participation of a histidine residue [74],... 

The principle advances in the area has been made using x-ray structural analysis. Crystallographic data have been first produced for the nitrogenase complex of FeP (A2) and FeMoP (Al) from Azotobacter vinelandii (Kim and Rees, 1992) and for the corresponding complex of Cp2 and Cpl from Clostridium pasterianum (Bolen et al., 1993), ). A 1.6 A resolution X-ray crystallographic structure of Klebsiella pneumoniae proteins has been recently reported (Mayer et al., 1999) It was shown that FeMoco sites in Al, Cpl, and Kpl are 70 A apart and FeMoco and P clusters are separated by about 19 A. X-ray structures of the nitrogenase complex and the active site clusters are presented in (Figs. 3.2-3.4). 

Rubredoxin is a small protein which has one Fe ion (molecular weight 6000), as is schematically illustrated in Fig. 3. Jensen s group has revealed fairly precise structural features of the active site of Clostridium pasteurianum and Desulfovibrio vulgaris rubredoxins (10, 11). The simple model complex [Fe(S2-o-xyl)2], 2 has been synthesized and analyzed crystallographically by Holm s group (12). Geometry of the FeS4 core of the oxidized rubredoxin seems to be almost identical to that... 

Fe-S Bond Lengths and Fe-S-C Angles of the Active Site of Clostridium pasteurianum Rubredoxin with 1.2-A Refinement X-Ray Analysis... 

Many microbes contain a hydrogenase that lacks nickel. The best studied of these proteins is the hydrogenase from C. pasteurianum (Adams, 1990). The active site of this protein has been called the H cluster. Two structures of this protein recently appeared, a 1.6 structure of the het-erodimeric Desulfovibrio desuljuricans enzyme (Nicolet et al., 1999) and the 1.8 structure of the Cpl enzyme from Clostridium pasteurianum (Peters et al., 1998). The H cluster at the active site contains 6Fe as proposed earlier (Adams et al., 1989). There are two subcomponents a typical [4Fe64S] cubane bridged by a cysteine residue to an active site binuclear Fe center (Figure 4b). The unusual nature of the iron site in the NiFe hydrogenase is... 

Figure 1 (a) A schematic drawing of the active site of [NiFe] hydrogenases as deduced from the crystallographic studies. (h) A schematic drawing of the H-cluster of the CO-inhihited form of the Clostridium pasteurianum [Fe] hydrogenases as deduced from the recent X-ray crystallographic studies " ... 

Recently, a glycerol dehydratase was discovered in the anaerobic bacterium Clostridium butyricum, whose active site contains a glycyl radical formed by the action of the 5 -deoxyadenosyl radical on a specific glycine residue of the protein (20). The 5 -deoxyadenosyl radical is generated not from coenzyme Bi2, but by one-electron reduction of the stmcturally much simpler molecule 5-adenosylmethionine (SAM), named poor man s B12 by Barker. Hence, this glycerol dehydratase performs the same reaction, probably with a similar pathway, to the coenzyme B 12-dependent glycerol dehydratase. 

Behmer J, Jung M, Sehr P et al. (1996) Active site mutation of the C3-like ADP-ribosyltronsferose from Clostridium limosum - Analysis of glutamic acid 174. In Biochemistry 35 282-9... 

CE Family 1 is very large and contains members which do not act on carbohydrate-derived substrates. The crystal structure of a CE 1 domain of XynlOB modular enzyme from Clostridium thermocellum has been solved. " The CE 1 domain is a feruloyl esterase which hydrolyses the feruloyl groups attached to some arabinofuranosyl 05 groups in native xylan. (The Xyn lOB protein as a whole consists of two CBM 22 domains, a dockerin domain, and a GH 20 xylanase domain, and forms part of a cellulosome - see Section 5.10.) The enzyme has the common a/p hydrolase fold. Studies of ferulic acid complexes of the inactive alanine mutant of the active site serine revealed the classic catalytic triad, and two main-chain peptide NH bonds are in place to form an oxyanion hole . A remarkable feature is that the enzyme as repeatedly isolated was esterilied on the active site serine by phosphate or sulfate. 

LAM from Clostridium subterminale in complex with the substrate crystallizes as a homotetramer with domain-swapped dimers stabilized by structural zinc ions. Each monomer contains one active site, which is a channel defined by a P / a) -crescent and binds a molecule of PLP, a molecule of SAM, and a [4Fe-4S] cluster. In the active site the external aldimine of PLP with lysine, SAM, and the Fe-S cluster lie spatially close (Figure 29), supporting the idea that the formation of the 5 -deoxyadenosyl radical and the abstraction of the... 

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