View source for Structure of 1zkd

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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.

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

[[Image:2ex4 jmol.JPG|thumb|2ex4|left]]

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

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
































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
  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


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

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

























Ligang Binding Sites

[http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=SAH&sid=2EX4 S-ADENOSYL-L-HOMOCYSTEINE]is found on the 2 methyltranferases.











==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]]


===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