Tyrosine phosphorylation is catalyzed by protein tyrosine kinases, which are represented by 90 genes in the human genome. Here, we present the set of 107 genes in the human genome that encode members of the four protein tyrosine phosphatase (PTP) families. The four families of PTPases, their substrates, structure, function, regulation, and the role of these enzymes in human disease will be discussed.

We applied a new multi-step protocol to predict the structures of all targets during CASP5, regardless of their potential category. 1) We used diverse fold-recognition (FR) methods to generate initial target-template alignments, which were converted into preliminary full-atom models by comparative modeling. All preliminary models were evaluated (scored) by VERIFY3D to identify well- and poorly-folded fragments. 2) Preliminary models with similar 3D folds were superimposed, poorly-scoring regions were deleted and the "average model" structure was created by merging the remaining segments. All template structures reported by FR were superimposed and a composite multiple-structure template was created from the most conserved fragments. 3). The average model was superimposed onto the composite template and the structure-based target-template alignment was inferred. This alignment was used to build a new (intermediate) comparative model of the target, again scored with VERIFY3D. 4) For all poorly scoring regions series of alternative alignments were generated by progressively shifting the "unfit" sequence fragment in either direction. Here, we considered additional information, such as secondary structure, placement of insertions and deletions in loops, conservation of putative catalytic residues, and the necessity to obtain a compact, well-folded structure. For all alternative alignments, new models were built and evaluated. 5) All models were superimposed and the "FRankenstein's monster" (FR, fold recognition) model was built from best-scoring segments. The final model was obtained after limited energy minimization to remove steric clashes between sidechains from different fragments. The novelty of this approach is in the focus on "vertical" recombination of structure fragments, typical for the ab initio field, rather than "horizontal" sequence alignment typical for comparative modeling. We tested the usefulness of the "FRankenstein" approach for non-expert predictors: only the leader of our team had considerable experience in protein modeling - he registered as a separate group (020) and submitted models built only by himself. At the onset of CASP5, the other five members of the team (students) had very little or no experience with modeling. They followed the same protocol in a deliberately naïve way. In the fourth step they used solely the VERIFY3D criterion to compare their models and the leader's model (the latter regarded only as one of the many alternatives) and generated the hybrid or selected only one model for submission (group 517). In order to compare our protocol with the traditional "one target-one template-one alignment" approach, we submitted (as a separate group 242) models selected from those automatically generated by all CAFASP servers (i.e. obtained without any human intervention). Here, we compare the results obtained by the three "groups", describe successes and failures of the "FRankenstein" approach and discuss future developments of comparative modeling. The automatic version of our multi-st...

In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts.

COLORADO3D is a World Wide Web server for the visual presentation of three-dimensional (3D) protein structures. COLORADO3D indicates the presence of potential errors (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), identifies buried residues and depicts sequence conservations. As input, the server takes a file of Protein Data Bank (PDB) coordinates and, optionally, a multiple sequence alignment. As output, the server returns a PDB-formatted file, replacing the B-factor column with values of the chosen parameter (structure quality, residue burial or conservation). Thus, the coordinates of the analyzed protein 'colored' by COLORADO3D can be conveniently displayed with structure viewers such as RASMOL in order to visualize the 3D clusters of regions with common features, which may not necessarily be adjacent to each other at the amino acid sequence level. In particular, COLORADO3D may serve as a tool to judge a structure's quality at various stages of the modeling and refinement (during both experimental structure determination and homology modeling). The GeneSilico group used COLORADO3D in the fifth Critical Assessment of Techniques for Protein Structure Prediction (CASP5) to successfully identify well-folded parts of preliminary homology models and to guide the refinement of misthreaded protein sequences. COLORADO3D is freely available for academic use at http://asia.genesilico.pl/colorado3d/.

The smallest active protein-tyrosine phosphatase yet (only 16 kDa) is described here and given the name VHZ for VH1-like member Z because it belongs to the group of small Vaccinia virus VH1-related dual specific phosphatases exemplified by VHR, VHX, and VHY. Human VHZ is remarkably well conserved through evolution as it has species orthologs in frogs, fish, fly, and Archaea. The gene for VHZ, which we designate as DUSP25, is located on human chromosome 1q23.1 and consists of only two coding exons. VHZ is broadly expressed in tissues and cells, including resting blood lymphocytes, Jurkat T cells, HL-60, and RAMOS. In transfected cells, VHZ was located in the cytosol and in other cells also in the nucleoli. Endogenous VHZ showed a similar but more granular distribution. We show that VHZ is an active phosphatase and analyze its structure by computer modeling, which shows that in comparison with the 185-amino acid residue VHR, the 150-residue VHZ is a shortened version of VHR and contains the minimal set of secondary structure elements conserved in all known phosphatases from this class. The surface charge distribution of VHZ differs from that of VHR and is therefore unlikely to dephosphorylate mitogen-activated protein kinases. The remarkably high degree of conservation of VHZ through evolution may indicate a role in some ancient and fundamental physiological process.The VH1-like phosphatases (1) are members of the cysteinebased protein-tyrosine phosphatase (PTP) 1 family and contain the extended consensus signature motif DX 27-30 HCX 2 GX 2 R(S/ T/A)X 5 A(Y/F)LM or slight variations thereof. The crystal structures of the catalytic domains of the VH1-like enzymes VHR (2), mitogen-activated protein kinase phosphatase-3 (MKP-3) (3), KAP (4), PTEN (5), and MTMR2 (6) show that they have the same topology and catalytic machinery as other members of the Class I cysteine-based PTP family exemplified by PTP1B (7) and RPTP␣ (8). However, whereas the catalytic cleft of most VH1-like phosphatases is only 6 Å deep to allow access by the shorter phosphoamino acid side chains of phosphoserine (Ser(P)) and phosphothreonine (Thr(P)) to the catalytic Cys at the bottom of the pocket, the deeper (9 Å) pocket of classical phosphatases like PTP1B only permits dephosphorylation of phosphotyrosine. On the other hand, the catalytic pockets of PTEN (5) and MTMR2 (6) are considerably wider to accommodate their unique physiological substrate, the lipid-bound inositol ring with phosphate at the D position.VH1-like phosphatases are found in all main classes of organisms from bacteria to plants, yeast, insects, worms, and mammals. The human and mouse genomes each encode at least 61 VH1-like enzymes 2 , 11 of which are collectively referred to as the MKPs. In addition to a catalytic VH1-like domain, these MKPs contain a non-catalytic CDC25 homology (CH2) domain for docking with mitogen-activated protein kinases (10), which subsequently are dephosphorylated by the catalytic domain. Another group of 19 small VH1-like phosphatases lack the CH2 doma...