Structure of 1zkd: Difference between revisions

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__TOC__
__TOC__


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.
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:1zkd jmol.JPG|1zkd|left]]


[[Image:2ex4 asym r 250.jpg|thumb|2ex4|left]]
[[Image:2ex4 jmol.JPG|2ex4|left]]
 
[[Image:1im8 jmol.JPG|1im8|left]]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


[[Image:1im8 bio r 250.jpg|thumb|1im8|left]]


[[Image:1im8 bio r 251.jpg|thumb|1im8|left]]




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[[Image:Structure aling.JPG|thumb|Structure Alignment With 2ex4|left]]
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]]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 


[[Image:Structure alig.JPG|thumb|Structure Alignment with 1im8|left]]




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Ligang Binding Sites
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.
[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]]




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==Sequence==
MIDQTALATEIKRLIKAAGPMPVWRYMELCLGHPEHGYYVTRDPLGREGDFTTSPEISQMFGELLGLWSASVWKAADEPQ
TLRLIEIGPGRGTMMADALRALRVLPILYQSLSVHLVEINPVLRQKQQTLLAGIRNIHWHDSFEDVPEGPAVILANEYFD
VLPIHQAIKRETGWHERVIEIGASGELVFGVAADPIPGFEALLPPLARLSPPGAVFEWRPDTEILKIASRVRDQGGAALI
IDYGHLRSDVGDTFQAIASHSYADPLQHPGRADLTAHVDFDALGRAAESIGARAHGPVTQGAFLKRLGIETRALSLMAKA
TPQVSEDIAGALQRLTGEGRGAMGSMFKVIGVSDPKIETLVALSDDTDREAERRQGTHGLEHHHHHH




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==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==
==Information on 1zkd==

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.

1zkd
2ex4
1im8
































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 aling.JPG




























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

Structure Alignment with 1im8


























Ligang Binding Sites

SELENOMETHIONINE is found on 1zkd.

S-ADENOSYL-L-HOMOCYSTEINEis found on the 2 methyltranferases.


Binding sites.JPG
Ligand.JPG














































Surface Properties

Red shows negatively charge and blue shows positively charge

Surface charge.JPG


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

Article on 1im8

Most probably a methyltransferase as most of the matches from DALI are transferase

Left

Left


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