Structure ERp18: Difference between revisions
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'''Figure 2:''' PyMOL image (front view) displaying conserved surface residues, which | '''Figure 2:''' PyMOL image (front view) displaying conserved surface residues, which surround the location of the cysteine residues. These conserved surface residues are hypothesised to form the active site of ERp18. Conserved regions on this front view are shown in pink, green, yellow, and dark blue. These regions correspond to continuous segments of highly conserved amino acids. | ||
[[Image: Image_2.png]] | [[Image: Image_2.png]] | ||
Figure | '''Figure 3:''' PyMOL image (rear view) displaying another area of conservation. This area is not believed to have any catalytic activity; nevertheless, it is likely to have an important function. | ||
Revision as of 10:31, 11 June 2009
Methods
Study of the ERp18 protein (ID = 1sen) began by downloading its file from the Protein Data Bank (PDB) and visualising it using PyMOL. It was known from study about its function that ERp18 contains a CXXC motif, characteristic of all thiol-disulfide oxidoreductases - this motif was identified as 66-CGAC-69 on ERp18. These cysteine residues were localised to the surface of the protein and were predicted to form the catalytic site. Next, conserved sequences identified by a ClustalW multiple alignment from evolution study were highlighted on the protein, both surface and ribbon models were used. Following this, searches were made with PDBsum and SCOP. Secondary structures were provided by PDBsum. After completing these fundamental protein structure searches, literature from PubMed was viewed and findings from this study were compared with those made in the literature.
Results
Figure 1: PyMOL image displaying the catalytic cysteine residues (66,69) of ERp18. These residues fit the CXXC motif ubiquitous of all thiol–disulfide oxidoreductases.
Figure 2: PyMOL image (front view) displaying conserved surface residues, which surround the location of the cysteine residues. These conserved surface residues are hypothesised to form the active site of ERp18. Conserved regions on this front view are shown in pink, green, yellow, and dark blue. These regions correspond to continuous segments of highly conserved amino acids.
Figure 3: PyMOL image (rear view) displaying another area of conservation. This area is not believed to have any catalytic activity; nevertheless, it is likely to have an important function.
Figure 3: PyMOL image displaying the conserved sections of a ribbon diagram of ERp18. Notice the conservation of the three core beta sheets - probably vital for maintaining stability and correct folding of the protein.
Dali Summary
No: Chain Z rmsd lali nres %id PDB Description 1: 1sen-A 31.6 0.0 134 134 100 PDB MOLECULE: THIOREDOXIN-LIKE PROTEIN P19; 2: 3f9u-A 13.0 2.2 114 145 12 PDB MOLECULE: PUTATIVE EXPORTED CYTOCHROME C BIOGENESIS- 3: 3f9u-B 12.3 2.2 114 148 12 PDB MOLECULE: PUTATIVE EXPORTED CYTOCHROME C BIOGENESIS- 4: 2fwe-A 11.7 2.4 107 122 21 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 5: 2fwf-A 11.6 2.4 107 123 21 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 6: 1se1-C 11.1 2.1 103 231 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 7: 1vrs-F 11.1 2.1 103 118 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 8: 1vrs-D 11.1 2.2 102 118 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 9: 1se1-A 11.1 2.2 102 239 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 10: 1ep7-B 10.9 2.4 102 112 13 PDB MOLECULE: THIOREDOXIN CH1, H-TYPE; 11: 2fwg-A 10.9 2.7 106 122 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 12: 2fwh-A 10.9 2.2 102 117 23 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 13: 1uc7-A 10.8 2.2 104 124 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 14: 1ep8-B 10.8 2.5 103 112 13 PDB MOLECULE: THIOREDOXIN CH1, H-TYPE; 15: 1ep8-A 10.7 2.5 103 112 13 PDB MOLECULE: THIOREDOXIN CH1, H-TYPE; 16: 2ju5-A 10.6 2.2 105 144 17 PDB MOLECULE: THIOREDOXIN DISULFIDE ISOMERASE; 17: 1ep7-A 10.6 2.6 103 112 13 PDB MOLECULE: THIOREDOXIN CH1, H-TYPE; 18: 1vrs-E 10.6 2.2 102 118 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 19: 1uc7-B 10.5 2.3 104 124 23 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 20: 3d22-A 10.4 2.8 108 129 13 PDB MOLECULE: THIOREDOXIN H-TYPE; 21: 3d21-A 10.4 2.5 101 111 16 PDB MOLECULE: THIOREDOXIN H-TYPE; 22: 3d21-B 10.3 2.5 101 111 16 PDB MOLECULE: THIOREDOXIN H-TYPE; 23: 3fk8-A 10.2 2.6 106 131 17 PDB MOLECULE: DISULPHIDE ISOMERASE; 24: 2vlv-B 10.2 2.3 99 113 22 PDB MOLECULE: THIOREDOXIN H ISOFORM 2.; 25: 1se1-B 10.2 2.2 102 243 22 PDB MOLECULE: THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD; 26: 2vlu-B 10.2 2.3 100 112 22 PDB MOLECULE: THIOREDOXIN H ISOFORM 2.; 27: 2vm1-A 10.2 2.3 99 110 16 PDB MOLECULE: THIOREDOXIN H ISOFORM 1.; 28: 2vlv-A 10.1 2.4 100 111 22 PDB MOLECULE: THIOREDOXIN H ISOFORM 2.; 29: 2vm2-A 10.1 2.3 99 109 16 PDB MOLECULE: THIOREDOXIN H ISOFORM 1.; 30: 2vlt-B 10.1 2.4 100 110 22 PDB MOLECULE: THIOREDOXIN H ISOFORM 2.;
Figure 4: The top thirty hits from a DALI search with 1sen-A. DALI lists proteins in order of their structural similarity. The protein names displayed are almost entirely thiol:disulfide interchange proteins and thioredoxins (thioredoxins being a related protein to the catalytic domain of thiol:disulfide interchange proteins), with the exception of 'putative exported cytochrome c biogenesis-related protein' for 2 and 3. However, hits 2 and 3 contain the CXXC motif and are therefore likely to be members of the thioredoxin family.
PDBsum
PDB id: 1sen Name: Structural genomics, unknown function Title: Endoplasmic reticulum protein rp19 o95881
Structure: Thioredoxin-like protein p19. Chain: a. Synonym: endoplasmic reticulum protein erp19. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: tlp19. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the protein was cloned, expressed and purified by the secsg human protein production group (t.A. Dailey, m. Mayer) under the direction of h.A. Dailey.
UniProt: O95881 (TXD12_HUMAN) SAS Seq: 172 a.a. Struc: 135 a.a. Key: PfamB domain Secondary structure CATH domain
Enzyme class: E.C.1.8.4.2 [IntEnz] [ExPASy] [KEGG] [BRENDA]
Reaction: 2 glutathione + protein-disulfide = glutathione disulfide + protein- dithiol (see diagram below)
Resolution: 1.20Å
R-factor: 0.162
R-free: 0.183
Authors: Z.-J.Liu,L.Chen,W.Tempel,A.Shah,D.Lee,T.A.Dailey,M.R.Mayer, J.P.Rose,D.C.Richardson,J.S.Richardson,H.A.Dailey,B.-C.Wang Southeast Collaboratory For Structural Genomics (Secsg)
Key ref: z.-j.liu et al. Endoplasmic reticulum protein Rp19. To be Published, xsi:nil="true" />.
Date: 17-Feb-04
Release date: 13-Jul-04
Related entries: O95881 related db: targetdb
Figure 5: Secondary Structure of 1sen produced by PDBsum
Figure 6: Secondary Structure of 3f9u produced by PDBsum
SCOP Summary
Protein: Thioredoxin-like protein p19, TLP19 from Human (Homo sapiens) [TaxId: 9606] Lineage:
1. Root: scop
2. Class: Alpha and beta proteins (a/b) [51349]
Mainly parallel beta sheets (beta-alpha-beta units)
3. Fold: Thioredoxin fold [52832]
core: 3 layers, a/b/a; mixed beta-sheet of 4 strands, order 4312; strand 3 is antiparallel to the rest
4. Superfamily: Thioredoxin-like [52833]
5. Family: Thioltransferase [52834]
6. Protein: Thioredoxin-like protein p19, TLP19 [110604]
7. Species: Human (Homo sapiens) [TaxId: 9606] [110605]
Discussion
The localisation of the CXXC motif to a highly conserved surface region indicates that it forms the active site. Conservation of the internal B-sheets is probably vital for the correct conformation of the protein. Interestingly, a second surface region of high homology was identified (catalytic activity??). Interestingly, the literature identified ERp18 as a dimer.
