|General information||Species distribution||Numeration assumed||Sequence conservation||3D conservation||Contacts with DNA|
Together with Hbonds in this study possible water bridges, e.g. water
molecules mediating protein-DNA interaction, were analyzed. Water molecules were found
in 16 structures, representing 7 proteins;they are listed in the table below.
|Protein & species||Chains in the file with superimposed structures||DNA||Models|
|ETS-1 H. sapiens||G, H||No||7, 8|
|SAP-1 H. sapiens||A, B||Yes||1, 2|
|PDEF H. sapiens||Y||Yes||25|
|Elk-1 H. sapiens||D, E||Yes||4, 5|
|ETS-1 M. musculus||L, M, N, O, R, S||Yes/No||12, 13, 14, 15, 18, 19|
|PU.1 M. musculus||U, V||Yes||21, 22|
|GABP alpha M. musculus||C||Yes||3|
The detection of clusters of water molecules (CWM) was performed in the file with superimposed structures of ETS domain using program
wLake with distance threshold 1.5 Å and with 5 or more water molecules in a cluster.
Totally there were found 64 CWM, 15 of them turned out to be on protein-DNA interface, thus
being potentially able to form a water bridge. They were analyzed manually. Clusters wat10 and wat20 were united and called wat10, clusters wat29 and wat30 - wat30 respectively. Cluster wat53 was rejected, some of it's molecules being added to wat52. Finally 12 CWM were chosen and taken into analysis. The results are represented in the following table:
|wat39||asn327.od/ lys327.nz/ ser327.og||800.phosphate oxygen||A, B, D, E, V, Y||SAP-1, Elk-1, PDEF from H. sapiens, PU.1 from M. musculus|
|wat57||val51.o/ ile51.o; lys261.nz||837.phosphate oxygen||A, B, D, E, L, M, O, U, Y||SAP-1, Elk-1, PDEF from H. sapiens, ETS-1 and PU.1 from M. musculus|
|wat48||trp257.o; trp257.ne1; gly258.n||838.phosphate oxygen||A, B, D, E, L, M, N, Y||SAP-1, Elk-1, PDEF from H. sapiens, ETS-1 from M. musculus|
|wat22||pro303.n; lys304.n/ asn304.n/ ala304.n||839.phosphate oxygen||B, L, M, R, S, Y||SAP-1, PDEF from H. sapiens, ETS-1 from M. musculus|
|wat6||glu251.oe/ asp251.od||798.phosphate oxygen||B, D, E, L, N, O||SAP-1, Elk-1 from H. sapiens, ETS-1 from M. musculus|
|wat15||lys302.nz/ arg302.nh/ arg302.n||839.phosphate oxygen||A, B, L, M, U, Y||SAP-1, PDEF from H. sapiens, ETS-1, PU.1 from M. musculus|
|wat62||lys309.o||838.phosphate oxygen||A, B, C, D, E, L, N, O, U, V, Y||SAP-1, Elk-1, PDEF from H. sapiens, PU.1, ETS-1, GABP from M. musculus|
|wat10||arg315.o||801.phosphate oxygen||A, B, D, E, L, M, N, U, Y||SAP-1, Elk-1, PDEF from H. sapiens, PU.1, ETS-1 from M. musculus|
|wat36||ser311.og; arg315.nh||799.phosphate oxygen||A, B, D, E, L, M, N, O, U, V, Y||SAP-1, Elk-1, PDEF from H. sapiens, PU.1, ETS-1 from M. musculus|
|wat52||arg315.nh1; tyr355.oh||800.phosphate oxygen||A, B, C, D, E, N, O, S, U, V, Y||SAP-1, Elk-1, PDEF from H. sapiens, PU.1, ETS-1, GABP from M. musculus|
|wat50||asp308.o/ glu308.o; asp308.od||c840.n4; c841.n4||A, B, C, D, E, U, V, Y||SAP-1, Elk-1, PDEF from H. sapiens, PU.1, GABP from M. musculus|
|wat30||asp308.o; asp308.od; ser311.og; arg315.nh||c800.n4/ g800.n7||A, B, D, E, L, O, U, Y||SAP-1, Elk-1, PDEF from H. sapiens, PU.1, ETS-1 from M. musculus|
On the left there shown the overall picture of all 12 clusters of water molecules which might mediate protein-DNA interaction. Water molecules are represented as green balls, alpha-helices of the example ETS structure are red, while beta-strands are yellow.
Most of the AA residues participating in water mediated interaction make contacts by their backbone atoms, while 6 of them make contacts by their sidechain atoms. 5 of these residues (251, 302, 311, 327, 355) make no other contacts with DNA, so their conservation could indicate the importace of the particular water bridge in DNA binding ability of the domain.
Tyr355 is the most conservative ofthese residues, it can be found in 94.64% (according to Pfam alignment) of sequences. It contacts to cluster wat52, which is also very conservative according to our data.
Ser311 can be found in 77.58% of sequences, in other cases this position is occupied by Gly or Ala. It contacts to clusters wat30 and wat36.
In position 251 there can be found Glu (44.08%), Asp (31.99%) or Lys (14.11%). Any of these residues has possibility to make contact to cluster wat6 by it's sidechain atoms.
Position 302 is most often occupied by Lys (60.71%) or Arg (27.2%) which contacts to cluster wat15. Sometimes (in chain U) it makes contact not by sidechain atom but backbone nitrogen.
Residue 327 is not conservative and can be represented by various amino acids, some of which has hydrophobic sidechains and cannot contact to a water molecule.
To see the picture of a particular water cluster click on it's name in the table above.
Download Rasmol script for defining conservative clusters of water molecules
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