Structure of 1zkd

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.

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

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