Study of the DcpS Family

Study of theStudy of the

DcpS FamilyDcpS FamilyMarch 5th 2009

Structural Bioinformatics

Msc BIOINFO, UPF

Salvador Jesús Capella Gutiérrez

Juan Ramón Meneu Hernández

Rut Carolina Morata Gil

Main SchemeMain Scheme

1) Main Approachesa) Initial Purpose: P-Bodiesb) Second Purpose: HIT Familyc) Final Purpose: DcpS Family

2) DcpS Familya) Biological Aspectsb) Basic Analysisc) Extended Analysis

11stst PART: PART:

main approachesmain approaches

Initial Purpose: P-BodiesInitial Purpose: P-Bodies

P-Bodies are discrete cytoplasmic domains where several proteins involved in mRNA degradation, translational repression and some other related functions colocalize

Initial Purpose: P-BodiesInitial Purpose: P-Bodies

P-Bodies are discrete cytoplasmic domains where several proteins involved in mRNA degradation, translational repression and some other related functions colocalize

Constituted by proteins belonging to different families !!!

Look for the protein belonging to the family with more documented

structures: HIT Family

Pfam

Protein Family Interactions

Species Structures

DcpS HIT 1 932 33

SOLUTION

MAIN PROBLEM

second Purpose: hit familysecond Purpose: hit family

Histidine Triad / HIT Motif / HIT hexapeptide

H H H = Hydrophobic residue

>swissprot|Q96C86|DCPS_HUMANMADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

results

PSSM Matrix


TARGET

Blast against Uniref100

Blast against PDB

HMMPfam against PFAM

HMMSearch against PDB

Filter out mutated sequences

Select consensus sequences

DCPS_Human

+ target

DCPS Family

HMMFetch against PFAM

HMM Matrix + target

Mutagenesis Studies:

H H => N) H

Same Sequence. Different Substrates.

9 final structures for the HIT Family



ClustalW

Filter out mutated sequences

Select consensus sequences

T-Coffee StampAlignfit +

Stamp


9 final structures for the HIT

Family

Superposition turned out to be a real mess

!!!

ALIGNFIT + STAMPSTAMPSTAMPALIGNFIT + STAMP


Histidine Triad / HIT Motif / HIT hexapeptide

H H H = Hydrophobic residue

HIT Superfamily

Fhit DcpS Hint

Within each branch => High degree of conservation among

proteins

Between each branch => HIT MOTIF is the only region absolutely

conserved

9 final structures for the HIT

Family

Superposition turned out to be a real mess

!!!

DcpS Family

final Purpose: dcps familyfinal Purpose: dcps family

22ndnd PART: PART:

DCPS familyDCPS family

Biological aspectsBiological aspects

Main degradation pathway

In mammals, this family contains only one member, DcpS, which:

Stands for “scavenger mRNA decapping enzyme”

Hydrolyses the residual cap structure following 3' to 5' mRNA decay

Is the first member of the HIT family of proteins with a defined

biological function.


DcpS shares functional similarity with Dcp2:


Mutations in the HIT motif lead to the complete loss of

the function

The region (binding site) is critical for decapping activity

BASIC analysisBASIC analysis

Human (Homo sapiens)

Mouse (Mus musculus)

Yeast (Sacch. cerevisiae)

Rat (Rattus norvegicus)

Bovine (Bos taurus) Pig (Sus scrofa)

TARGET SEQUENCE(no PDB Structure)

TEMPLATES (PDB Structure)

Several orthologues have been studied:

BASIC ANALYSISBASIC ANALYSIS


1XMM

Human (Homo Sapiens)

+

1VLR


STAMP

86 % Sequence Identity



1XMM


+

1VLR



DALI



1XMM


+

1VLR



SAP


TARGET SEQUENCE (no PDB Structure)

>sp|Q8MIZ3|DCPS_PIG Scavenger mRNA-decapping enzyme DcpS OS=Sus scrofa GN=DCPS PE=2 SV=1MADTAPQPSKRKRERDPEEAEAPSTEEKEARVGNGTSAPVRLPFSGFRVKKVLRESARDKIIFLHGKVNEASGDGDGEDAIVILEKTPFQVDQVAQLLMGSPELQLQFSNDIYSTYHLFPPRQLSDVKTTVVYPATEKHLQKYLHQDLHLVRETGGDYKNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQKQLDDLYLIAICHRRGIKSLRDLTPEHLPLLRNILREGQEAILQRYQVTGDRLRVYLHYLPSYYHLHVHFTALGFEAPGAGVERAHLLAEVIENLEQDPEHYQRRTLTFALRADDPLLTLLQEAQRS


TARGET DCPS_Pig

ClustalW T-Coffee Stamp

+ DCPS Templates (2)


SwissModel


TARGET DCPS_Pig

ClustalW T-Coffee Stamp

+ DCPS Templates (2)


STAMPSTAMP

extended analysisextended analysis

DcpS protein HUMAN (337 AA)

DcpS N-terminal domain(40 - 145)

DcpS C-terminal domain(146 - 337)

HIT domain(268 - 279)

HIT MOTIF(275 - 279)


DcpS dimer in complex with m7GpppG where:

N-terminaldomain – swapped

dimer

C-terminaldomain dimer

Chain AChain B


After analysing the HIT domain, we go deep into…

DcpS N-terminal domain

DcpS C-terminal domain

>swissprot|Q96C86|DCPS_HUMAN Scavenger mRNA-decapping enzyme DcpS;MADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTLTFALRADDPLLKLLQEAQQS

… to look for hints on the specificity of DcpS


We do the analysis through 3 different approaches:

Sequence

Structure

Literature

BLAST DALIPubMed


Members of the DcpS Family


Sequence: BLAST

Predicted or putative proteins

(not reviewed)

No new information

related to other families



Structure: DALI

No new information


All the results are members of

the DcpS and HIT Families



Literature: PubMed

The C-Terminal DcpS Domain Is Related, but Distinct from the HIT Protein Family

“A DALI search of the Protein Data Bank revealed structural similarity between DcpS and a number of HIT proteins. ...”

“… . In addition and as noted above, the DcpS C-terminal domain is not sufficient for cap hydrolysis, indicating substantive differences between these protein families.”


Basically members of the

DcpS and HIT Families

No new information related to other families



Members of the DcpS FamilyPredicted or putative proteins

(not reviewed)

No new information



Sequence: BLAST


N-terminal domain shares structural

homology to NTF2-like proteins


Literature: PubMed

PDB search using DALI

Carotenoid binding protein (CBP)

Metazoan mRNA export factor p15

Yeast mRNA export factor Mex67



Literature: PubMed

DcpS

DALI



Literature: PubMed

DcpS

mRNA export factor p15

DALI



Literature: PubMed

DcpS

mRNA export factor p15Carotenoid binding prot (CBP)

DALI



Literature: PubMed

DcpS

mRNA export factor p15Carotenoid binding prot (CBP)mRNA export factor Mex67

DALI



Literature: PubMed

These NTF2-like proteins form HETERODIMERS


DcpS dimer in complex with m7GpppG where:

N-terminaldomain – swapped

dimer

C-terminaldomain dimer

Chain AChain B


Literature: PubMed

DcpS forms swapped – HOMODIMERS !!!



Literature: PubMed

“N-terminal domain shares structural homology to NTF2-like proteins …” BUT

“… DcpS domain swapped – dimer has a unique topology and organization, which is different from either Mex67/Mtr2 or p15/TAP complexes“Mex67/Mtr2 and p15/TAP have been implicated in mRNA export pathways …” BUT

“… Any functional significance to the DcpS N-terminal domain structure remains unclear. ”



Structure: DALI

A PDB search using DALI shows kind of structural homology with proteins belonging to some other

families

Further studies should

be carried out

Thank youThank you

Any questions?Any questions?

Study of the DcpS Family

Documents

Transcript of Study of the DcpS Family