Cysteine dioxygenase (CDO) catalyzes the oxidation of L-cysteine to cysteine sulfinic acid. Deficiencies in this enzyme have been linked to autoimmune diseases and neurological disorders. The x-ray crystal structure of CDO from Mus musculus was solved to a nominal resolution of 1.75 Å. The sequence is 91% identical to that of a human homolog. The structure reveals that CDO adopts the typical ␤-barrel fold of the cupin superfamily. The NE2 atoms of His-86, -88, and -140 provide the metal binding site. The structure further revealed a covalent linkage between the side chains of Cys-93 and Tyr-157, the cysteine of which is conserved only in eukaryotic proteins. Metal analysis showed that the recombinant enzyme contained a mixture of iron, nickel, and zinc, with increased iron content associated with increased catalytic activity. Details of the predicted active site are used to present and discuss a plausible mechanism of action for the enzyme.cupin ͉ cysteine metabolism ͉ O2-activation M ouse cysteine dioxygenase (CDO) catalyzes the initial step in the biochemical pathway used for oxidation of cysteine to sulfate (1), namely the oxidation of L-cysteine to cysteine sulfinic acid as shown in Fig. 1. The enzyme activity has important medical implications because elevated cysteine levels have been associated with Parkinson's and Alzheimer's diseases (2). High cysteine-to-sulfate ratios have been observed in patients suffering from systemic lupus erthematosus and rheumatoid arthritis (3, 4). Moreover, the Hallervorden-Spatz syndrome, a neurological disorder associated with iron accumulation, has been linked to a decline in CDO activity (5).CDO displays significant sequence identity with some members of the cupin superfamily (6), which have a conserved ␤-barrel fold and share two conserved sequence motifs: G(X) 5 HXH(X) 3,4 E(X) 6 G and G(X) 5 PXG(X) 2 H(X) 3 N (6-8).The two His and Glu residues from the first motif and the His from the second motif coordinate the metal ion in germin, the superfamily archetype (9). The Mus musculus CDO sequence contains the first motif with the exception of the glutamate, which is replaced by cysteine. This substitution is conserved in other eukaryotic CDOs. The second motif is less conserved, and only the His and Asn residues are present in the mouse CDO.CDO does not require an external reductant ( Fig. 1) and incorporates both oxygen atoms from O 2 (10), which justifies the dioxygenase classification, but relatively little else is known about the reaction mechanism. The recombinant enzyme from Rattus norvegicus has been purified and characterized by steadystate kinetics (11); the mouse enzyme investigated here has an identical sequence. Reconstitution of the rat apoenzyme with various transition metals confirmed that iron was required for activity, in accord with the earlier conclusions (1). Moreover, the recombinant rat enzyme was active without a second interacting factor, despite previous reports suggesting that additional components were required (12, 13).Here, we describe the x-ra...

The SurA protein facilitates correct folding of outer membrane proteins in gram-negative bacteria. The sequence of Escherichia coli SurA presents four segments, two of which are peptidyl-prolyl isomerases (PPIases); the crystal structure reveals an asymmetric dumbbell, in which the amino-terminal, carboxy-terminal, and first PPIase segments of the sequence form a core structural module, and the second PPIase segment is a satellite domain tethered approximately 30 A from this module. The core module, which is implicated in membrane protein folding, has a novel fold that includes an extended crevice. Crystal contacts show that peptides bind within the crevice, suggesting a model for chaperone activity whereby segments of polypeptide may be repetitively sequestered and released during the membrane protein-folding process.

The Escherichia coli SurA protein is a periplasmic molecular chaperone that facilitates correct folding of outer membrane porins. The peptide binding specificity of SurA has been characterized using phage display of heptameric peptides of random sequence. The consensus binding pattern of aromatic-polar-aromatic-nonpolar-proline amino acids emerges for both SurA and a SurA "core domain," which remains after deletion of a peripheral peptidyl-proline isomerase domain. Isothermal titration calorimetry with a high affinity heptameric peptide of sequence WEYIPNV yields peptide affinities in the range of 1-14 M for both SurA and its core domain. Although the peptide consensus aromaticpolar-aromatic-nonpolar-proline occurs infrequently in E. coli proteins, the less restrictive tripeptide motif aromatic-random-aromatic appears with greater-thanrandom frequency in outer membrane proteins and is prevalent in the "aromatic bands" of the porin ␤ barrel structures. Thus, SurA recognizes a peptide motif that is characteristic of integral outer membrane proteins.

Objective To study the relative risk (RR) of all‐cause and cause‐specific mortality in rheumatoid arthritis (RA) associated with body mass index (BMI), and to quantify the clinical and outcome consequences of abnormal BMI. Methods We studied mortality in 24,535 patients over 12.3 years, dividing patients into 3 age groups, <50, 50–70, and >70 years and fit Cox regression models separately within each age stratum. We used BMI categories of <18.5 kg/m2 (underweight), 18.5 to <25 kg/m2 (normal weight, reference category), 25 to <30 kg/m2 (overweight), and ≥30 kg/m2 (obesity). Results BMI ≥30 kg/m2 was seen in 63–68% and underweight in ∼2%. Reduction in the RR (95% confidence interval [95% CI]) for all‐cause (AC) and cardiovascular mortality was seen for overweight (AC 0.8 [95% CI 0.8, 0.9]) and obese groups (AC 0.8 [95% CI 0.7, 0.8]), with and without comorbidity adjustment. Underweight was associated with increased mortality risk (AC 1.9 [95% CI 1.7, 2.3]). By contrast, obesity produced profound changes in clinical variables. Compared with normal weight, the odds ratio in the obese group was 4.8 for diabetes mellitus, 3.4 for hypertension, 1.3 for myocardial infarction, 1.4 for joint replacement, and 1.9 for work disability. Total semiannual direct medical costs were $1,683 greater, annual household income $6,481 less, pain scores 1.1 units higher, Health Assessment Questionnaire 0.28 higher, and EuroQol utility 0.7 units lower in the obese. Conclusion Overweight and obesity reduce the RR of all‐cause and cardiovascular mortality across different age groups and durations of RA. By contrast, overweight and obesity are associated with substantial increased risks of comorbidity, total joint replacement, greater pain, medical costs, and decreased quality of life.

Aspartoacylase catalyzes hydrolysis of N-acetyl-L-aspartate to aspartate and acetate in the vertebrate brain. Deficiency in this activity leads to spongiform degeneration of the white matter of the brain and is the established cause of Canavan disease, a fatal progressive leukodystrophy affecting young children. We present crystal structures of recombinant human and rat aspartoacylase refined to 2.8-and 1.8-Å resolution, respectively. The structures revealed that the N-terminal domain of aspartoacylase adopts a protein fold similar to that of zinc-dependent hydrolases related to carboxypeptidases A. The catalytic site of aspartoacylase shows close structural similarity to those of carboxypeptidases despite only 10 -13% sequence identity between these proteins. About 100 C-terminal residues of aspartoacylase form a globular domain with a two-stranded ␤-sheet linker that wraps around the N-terminal domain. The long channel leading to the active site is formed by the interface of the N-and C-terminal domains. The C-terminal domain is positioned in a way that prevents productive binding of polypetides in the active site. The structures revealed that residues 158 -164 may undergo a conformational change that results in opening and partial closing of the channel entrance. We hypothesize that the catalytic mechanism of aspartoacylase is closely analogous to that of carboxypeptidases. We identify residues involved in zinc coordination, and propose which residues may be involved in substrate binding and catalysis. The structures also provide a structural framework necessary for understanding the deleterious effects of many missense mutations of human aspartoacylase.N-acetyl-L-aspartate ͉ x-ray structure ͉ zinc-dependent hydrolase

This work provides a systematic comparison of vibrational CD (VCD) and electronic CD (ECD) methods for spectral prediction of secondary structure. The VCD and ECD data are simplified to a small set of spectral parameters using the principal component method of factor analysis (PC/FA). Regression fits of these parameters are made to the X-ray-determined fractional components (FC) of secondary structure. Predictive capability is determined by computing structures for proteins sequentially left out of the regression. All possible combinations of PC/FA spectral parameters (coefficients) were used to form a full set of restricted multiple regressions with the FC values, both independently for each spectral data set as well as for the two VCD sets and all the data grouped together. The complete search over all possible combinations of spectral parameters for different types of spectral data is a new feature of this study, and the focus on prediction is the strength of this approach. The PC/FA method was found to be stable in detail to expansion of the training set. Coupling amide I1 to amide I' parameters reduced the standard deviations of the VCD regression relationships, and combining VCD and ECD data led to the best fits. Prediction results had a minimum error when dependent on relatively few spectral coefficients. Such a limited dependence on spectral variation is the key finding of this work, which has ramifications for previous studies as well as suggests future directions for spectral analysis of structure. The best ECD prediction for helix and sheet uses only one parameter, the coefficient of the first subspectrum. With VCD, the best predictions sample coefficients of both the amide I' and I1 bands, but error is optimized using only a few coefficients. In this respect, ECD is more accurate than VCD for a-helix, and the combined VCD (amide I'+II) predicts the P-sheet component better than does ECD. Combining VCD and ECD data sets yields exceptionally good predictions by utilizing the strengths of each. However, the residual error, its distribution, and, most importantly, the lack of dependence of the method on many of the significant components derived from the spectra leads to the conclusion that the heterogeneity of protein structure is a fundamental limitation to the use of such spectral analysis methods. The underutilization of these data for prediction of secondary structure suggests spectral data could predict a more detailed descriptor.

The structure of the UDP-glucose pyrophosphorylase encoded by Arabidopsis thaliana gene At3g03250 has been solved to a nominal resolution of 1.86 Å. In addition, the structure has been solved in the presence of the substrates/products UTP and UDP-glucose to nominal resolutions of 1.64 Å and 1.85 Å. The three structures revealed a catalytic domain similar to that of other nucleotidyl-glucose pyrophosphorylases with a carboxy-terminal β-helix domain in a unique orientation. Conformational changes are observed between the native and substrate-bound complexes. The nucleotide binding loop and the carboxy-terminal domain, including the suspected catalytically important Lys360, move in and out of the active site in a concerted fashion. TLS refinement was employed to initially model conformational heterogeneity in the UDP-glucose complex followed by the use of multiconformer refinement for the entire molecule. Normal mode analysis generated atomic displacement predictions in good agreement in magnitude and direction with the observed conformational changes and anisotropic displacement parameters generated by TLS refinement. The structures and the observed dynamic changes provide insight into the ordered mechanism of this enzyme and previously described oligomerization effects on catalytic activity.

The protein from Arabidopsis thaliana gene locus At1g79260.1 is comprised of 166-residues and is of previously unknown function. Initial structural studies by the Center for Eukaryotic Structural Genomics (CESG) suggested that this protein might bind heme, and consequently, the crystal structures of apo and heme-bound forms were solved to near atomic resolution of 1.32 Å and 1.36 Å respectively. The rate of hemin loss from the protein was measured to be 3.6 × 10 −5 s −1 , demonstrating that it binds heme specifically and with high affinity. The protein forms a compact ten-stranded β-barrel that is structurally similar to the lipocalins and fatty acid binding proteins (FABPs). One group of lipocalins, the nitrophorins (NP), are heme proteins involved in nitric oxide (NO) transport and show both sequence and structural similarity to the protein from At1g79260.1 and two human homologues, all of which contain a proximal histidine capable of coordinating a heme iron. Rapid-mixing and laser photolysis techniques were used to determine the rate constants for carbon monoxide (CO) binding to the ferrous form of the protein (k' CO = 0.23 µM −1 s −1 , k CO = 0.050 s −1 ) and NO binding to the ferric form ( k' NO = 1.2 µM −1 s −1 , k NO = 73 s −1 ). On the basis of both structural and functional similarity to the nitrophorins, we have named the protein nitrobindin and hypothesized that it plays a role in NO transport. However, one of the two human homolog of nitrobindin contains a THAP domain, implying a possible role in apoptosis.