Bioinformatics Course

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Bioinformatics Course

Sao Paulo, Brazil,
June 9
-
11, 2011

Answers Exercise
s

UniProtKB
, Day 1



Exercise 5: Discover UniProt I


Have a look at the Glucocorticoid receptor protein in UniProt (P04150) and answer the following
questions:


(a) What is the
status of this entry: manually reviewed or unreviewed?


This is a UniProtKB/Swiss
-
Prot entry, which has been manually reviewed.


(b) What is the function of the protein?

Receptor for glucocorticoids (GC). Has a dual mode of action: as a transcription facto
r that binds
to glucocorticoid response elements (GRE) and as a modulator of other transcription factors.
Affects inflammatory responses, cellular proliferation and differentiation in target tissues. Could
act as a coactivator for STAT5
-
dependent transcrip
tion upon growth hormone (GH) stimulation
and could reveal an essential role of hepatic GR in the control of body growth. Involved in
chromatin remodeling. Plays a significant role in transactivation. Involved in nuclear
translocation
.


(c) What is the sub
cellular location of the protein?


Cytoplasm. Nucleus. Note: Cytoplasmic in the absence of ligand, nuclear after ligand
-
binding.


(d) How many phosphorylated sites? How many phosphorylated sites have been experimentally proven
to be phosphorylated? (hint:
look in the 'Sequence annotation' section)

1 Phosphothreonine, 9 phosphoserine (
May

2011), 2 sites have not been experimentally proven
for this human sequence (this sites are tagged 'By similarity')


(e) Compare the keywords and the Gene Ontology terms ass
ociated with the entry (see
http://www.uniprot.org/faq/23
)


See
http://www.ebi.ac.uk/QuickGO/GProtein?ac=P04150



(f) How many 3D structures are available for this protein ? Do they 'cover' all the protein sequence?


There are 9 3D structures corresponding to this protein sequence in PDB.
T
he 3D structures
cover amino acids 500
-
777, 521
-
777, 525
-
777, 528
-
777
respectively
.


(g) How many different protein sequences are available for this gene? Have they the same function?

This entry describes 9 isoforms produced by alternative splicing and alternative initiation.'



Exercise 6: Discover UniProt II


Have a look
at the Queuine tRNA
-
ribosyltransferase protein in UniProt (B3HCM8) and answer the
following questions:

(a) What is the status of this entry: manually reviewed or unreviewed?


This is a UniProtKB/TrEMBL entry, unreviewed = which has NOT been manually review
ed


(b) What are the name(s) of the gene and the name(s) of the protein?


Gene name: tgt; Protein name: Queuine tRNA
-
ribosyltransferase



(c) What is the function of the protein?

Exchanges the guanine residue with 7
-
aminomethyl
-
7
-
deazaguanine in tRNAs

with GUN
anticodons (tRNA
-
Asp,
-
Asn,
-
His and
-
Tyr). After this exchange, a cyclopentendiol moiety is
attached to the 7
-
aminomethyl group of 7
-
deazaguanine, resulting in the hypermodified
nucleoside queuosine (Q) (7
-
(((4,5
-
cis
-
dihydroxy
-
2
-
cyclopenten
-
1
-
yl
)amino)methyl)
-
7
-
deazaguanosine)


(d) Compare the keywords and the Gene Ontology terms associated with the entry.


See http://www.ebi.ac.uk/QuickGO/GProtein?ac=B3HCM8