Structure of 1zkd: Difference between revisions
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Result from [[DALI]] shows proteins that are similar to the 1zkd. They are [http://www.rcsb.org/pdb/explore/explore.do?structureId=2EX4 2ex4] and [http://www.rcsb.org/pdb/explore/explore.do?structureId=1IM8 1im8]. These 2 proteins matches 1zkd the most according to [[DALI]]. | Result from [[DALI]] shows proteins that are similar to the [http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZKD 1zkd]. They are [http://www.rcsb.org/pdb/explore/explore.do?structureId=2EX4 2ex4] and [http://www.rcsb.org/pdb/explore/explore.do?structureId=1IM8 1im8]. These 2 proteins matches [http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZKD 1zkd] the most according to [[DALI]]. The pictures below shows the structures of the proteins related comparing to 1zkd. 1zkd is made up of 2 chains of proteins as shown in the picture. | ||
[[Image:1zkd jmol.JPG|1zkd|left]] | |||
[[Image:2ex4 jmol.JPG|2ex4|left]] | |||
[[Image:1im8 jmol.JPG|1im8|left]] | |||
| Line 37: | Line 66: | ||
[http://www.rcsb.org/pdb/explore/explore.do?structureId=2EX4 | With these informations we can now look into the proteins that is similar to [http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZKD 1zkd] and predict the functions. [http://www.rcsb.org/pdb/explore/explore.do?structureId=1IM8 1im8] is found to be a [http://www.rcsb.org/pdb/explore/pubmed.do?structureId=1IM8 methyltransferase with a bound S-adenosylhomocysteine] from the crystal structure of YecO from Haemophilus influenzae (HI0319). [http://www.rcsb.org/pdb/explore/explore.do?structureId=2EX4 2ex4]is a human methyltransferase with S-adenosylhomocysteine. | ||
Alignment with 2ex4 | Alignment with 2ex4 | ||
| Line 59: | Line 84: | ||
2EX4:A 191/175 GVILDD---------------VDSSVCRDLDVVRRIICSAG---LSLLAEERQE | 2EX4:A 191/175 GVILDD---------------VDSSVCRDLDVVRRIICSAG---LSLLAEERQE | ||
Alignment with 1im8 | Alignment with 1im8 | ||
| Line 74: | Line 95: | ||
1IM8:A 157/155 ---NPNGVLVLSEKF | 1IM8:A 157/155 ---NPNGVLVLSEKF | ||
[http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=SAH&sid=2EX4 S-ADENOSYL-L-HOMOCYSTEINE | Structure Alignment with 2ex4 (Blue:1zkd, Purple: 2ex4) | ||
Alignment Length: 294 | |||
Gaps (average per molecule): 53.5 | |||
Sequence Identity: 14.4% | |||
RMSD min – max: 3.03A | |||
[[Image:Structure aling.JPG|left]] | |||
Structure Alignment with 1im8 (Blue:1zkd, Purple: 1im8) | |||
Alignment Length: 195 | |||
Gaps (average per molecule): 38.5 | |||
Sequence Identity: 11% | |||
RMSD min – max: 2.3A | |||
[[Image:Structure alig.JPG|Structure Alignment with 1im8|left]] | |||
Ligang Binding Sites | |||
[http://www.rcsb.org/pdb/ligand/ligandsummary.do?handler=biologyChemistry&hetId=MSE SELENOMETHIONINE] is found on 1zkd. | |||
[http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=SAH&sid=2EX4 S-ADENOSYL-L-HOMOCYSTEINE]is found on the 2 methyltranferases. | |||
[[Image:Binding sites.JPG|left]] | |||
[[Image:Ligand.JPG|left]] | |||
==Surface Properties== | |||
Red shows negatively charge and blue shows positively charge | |||
[[Image:Surface_charge.JPG|left]] | |||
==Sequence== | |||
MIDQTALATEIKRLIKAAGPMPVWRYMELCLGHPEHGYYVTRDPLGREGDFTTSPEISQMFGELLGLWSASVWKAADEPQ | |||
TLRLIEIGPGRGTMMADALRALRVLPILYQSLSVHLVEINPVLRQKQQTLLAGIRNIHWHDSFEDVPEGPAVILANEYFD | |||
VLPIHQAIKRETGWHERVIEIGASGELVFGVAADPIPGFEALLPPLARLSPPGAVFEWRPDTEILKIASRVRDQGGAALI | |||
IDYGHLRSDVGDTFQAIASHSYADPLQHPGRADLTAHVDFDALGRAAESIGARAHGPVTQGAFLKRLGIETRALSLMAKA | |||
TPQVSEDIAGALQRLTGEGRGAMGSMFKVIGVSDPKIETLVALSDDTDREAERRQGTHGLEHHHHHH | |||
==Information on 1zkd== | |||
Located on 2p22.2 on human chromosome with 441 aa | |||
Located on 17E3 on mouse chromosome with 436 aa | |||
[ | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=11746687 Article on 1im8] | ||
Most probably a methyltransferase as most of the matches from DALI are transferase | |||
[[Image:Struc.JPG|Left]] | |||
[[Image:InterPro.JPG|InterPro Scan Results|Left]] | |||
Latest revision as of 13:27, 5 June 2007
Result from DALI shows proteins that are similar to the 1zkd. They are 2ex4 and 1im8. These 2 proteins matches 1zkd the most according to DALI. The pictures below shows the structures of the proteins related comparing to 1zkd. 1zkd is made up of 2 chains of proteins as shown in the picture.
With these informations we can now look into the proteins that is similar to 1zkd and predict the functions. 1im8 is found to be a methyltransferase with a bound S-adenosylhomocysteine from the crystal structure of YecO from Haemophilus influenzae (HI0319). 2ex4is a human methyltransferase with S-adenosylhomocysteine.
Alignment with 2ex4 1ZKD:A 24/25 WRYXELCLGHPEHGYYV--TRDPLGREGDFTTSPEISQXFGELLGLWSASVWKAAD-EPQ 2EX4:A 24/7 IEDEKQFYS----KAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTG 1ZKD:A 81/82 TLRLIEIGPGRGTXXADALRALRVLPILYQSLSVHLVEINPVLRQKQQTLLAGI-RNIHW 2EX4:A 80/64 TSCALDCGAGIGRITKRLLLPL--------FREVDMVDITEDFLVQAKTYLGEEGKRVRN 1ZKD:A 140/141 HD-----SFEDVPEGPAVILANEYFDVLPIHQAIKRETGWHERVIEIGASGELVFGVAAD 2EX4:A 132/116 YFCCGLQDFTPEPDSYDVIWIQWVIGHLT------------------------------- 1ZKD:A 195/196 PIPGFEALLPPLARLSPPGAVFEWRP--DTEILKIASRVRDQGGAALIIDYG--HLRSDV 2EX4:A 161/145 ------------------------DQHLAEFLRRCKGSL-RPNGIIVIKDNMAQE----- 1ZKD:A 251/252 GDTFQAIASHSYADPLQHPGRADLTAHV---DFDALGRAAESIGARAHGPVTQG 2EX4:A 191/175 GVILDD---------------VDSSVCRDLDVVRRIICSAG---LSLLAEERQE
Alignment with 1im8 1ZKD:A 59/60 QXFGELLGLWSASVWKAADEPQTLRLIEIGPGRGTXXADALRALRVLPILYQSLSVHLVE 1IM8:A 42/40 SNIITAIGXLAERFV-----TADSNVYDLGCSRGAATLSARRNI-----NQPNVKIIGID 1ZKD:A 119/120 INPVLRQKQQTLLAGI---RNIHWHD--SFEDVPEGPAVILANEYFDVLPIHQAIKRETG 1IM8:A 92/90 NSQPXVERCRQHIAAYHSEIPVEILCNDIRHVEIKNASXVILNFTLQFLP---------- 1ZKD:A 174/175 WHERVIEIGASGELVFGVAADPIPGFEALLPPLARLSPPGAVFEWRP--DTEILKIASRV 1IM8:A 142/140 ---------------------------------------------PEDRIALLTKIYEGL 1ZKD:A 232/233 RDQG--GAALIIDYG 1IM8:A 157/155 ---NPNGVLVLSEKF
Structure Alignment with 2ex4 (Blue:1zkd, Purple: 2ex4)
Alignment Length: 294
Gaps (average per molecule): 53.5
Sequence Identity: 14.4%
RMSD min – max: 3.03A
Structure Alignment with 1im8 (Blue:1zkd, Purple: 1im8)
Alignment Length: 195
Gaps (average per molecule): 38.5
Sequence Identity: 11%
RMSD min – max: 2.3A
Ligang Binding Sites
SELENOMETHIONINE is found on 1zkd.
S-ADENOSYL-L-HOMOCYSTEINEis found on the 2 methyltranferases.
Surface Properties
Red shows negatively charge and blue shows positively charge
Sequence
MIDQTALATEIKRLIKAAGPMPVWRYMELCLGHPEHGYYVTRDPLGREGDFTTSPEISQMFGELLGLWSASVWKAADEPQ TLRLIEIGPGRGTMMADALRALRVLPILYQSLSVHLVEINPVLRQKQQTLLAGIRNIHWHDSFEDVPEGPAVILANEYFD VLPIHQAIKRETGWHERVIEIGASGELVFGVAADPIPGFEALLPPLARLSPPGAVFEWRPDTEILKIASRVRDQGGAALI IDYGHLRSDVGDTFQAIASHSYADPLQHPGRADLTAHVDFDALGRAAESIGARAHGPVTQGAFLKRLGIETRALSLMAKA TPQVSEDIAGALQRLTGEGRGAMGSMFKVIGVSDPKIETLVALSDDTDREAERRQGTHGLEHHHHHH
Information on 1zkd
Located on 2p22.2 on human chromosome with 441 aa
Located on 17E3 on mouse chromosome with 436 aa
Most probably a methyltransferase as most of the matches from DALI are transferase
Pfam Results
DUF185: domain 1 of 1, from 64 to 299: score 227.1, E = 3.9e-65
*->alArwllveykllgyPYadlnlvElGaGrGtaielmsdlLryiarlv
+l++w + ++k+ ++P l+l E+G+GrGt +m+d+Lr+ r+
query 64 LLGLWSASVWKAADEP-QTLRLIEIGPGRGT---MMADALRA-LRVL 105
PdvyartryylvEiSprLaarQketLapkvaplGhdskveieatdlsglv
P +y+ ++++lvEi+p L+++Q++ La ++ ++
query 106 PILYQSLSVHLVEINPVLRQKQQTLLA-----------------GIR-NI 137
rWhdasileedPdgvptvliaNEVlDalPHDlvrfdkrgggwyErhVlvd
Whd s +e++P+g p v++aNE +D lP +++ +kr+ gw+Er V ++
query 138 HWHD-S-FEDVPEG-PAVILANEYFDVLP--IHQAIKRETGWHER-V-IE 180
ldgdfrlvysqeldplaglaltlreaaldPVKstkklvpsalskllpkll
+ ++lv+++++dp g+ ++l
query 181 IGASGELVFGVAADPIPGFEAL------------------------LPPL 206
ppaeevgygtEvYsParllellqalaerLpahrGrlLaiDYGhlaseyyh
+ +g+++E+ P e+l+++ + + +G++L+iDYGhl+s
query 207 ARLSPPGAVFEW-RPDT--EILKIASRVRD-QGGAALIIDYGHLRSD--- 249
prrksalaaemfngtllqayrqhahddpltnpssllVlyStvaqGlaDiT
g+++qa+ h + dpl +p G+aD+T
query 250 ------------VGDTFQAIASHSYADPLQHP------------GRADLT 275
ahVDFtalaradqyqtaakaagdlkvlgvet<-*
ahVDF+al +aa +g + + g+ t
query 276 AHVDFDALG------RAAESIG-ARAHGPVT 299
