Structure ERp18: Difference between revisions

From MDWiki
Jump to navigationJump to search
No edit summary
No edit summary
Line 12: Line 12:
[[Image: Image_1.png]]
[[Image: Image_1.png]]


'''Figure 2:''' PyMOL image (front view) displaying conserved surface residues, which correspond to the location of the cysteine residues. These conserved surface residues are hypothesised to form the active site of ERp18.
'''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

Image of CC residues.png

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.


Image 1.png

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 2.png

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.


Image of ERp18 with conserved residues.png

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


Pdbsum 1senA.gif

Figure 5: Secondary Structure of 1sen produced by PDBsum


Pdbsum 3fpu.gif

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.