Structure of 1zkd: Difference between revisions

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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. 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]]
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
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]]




==Sequence==
MIDQTALATEIKRLIKAAGPMPVWRYMELCLGHPEHGYYVTRDPLGREGDFTTSPEISQMFGELLGLWSASVWKAADEPQ
TLRLIEIGPGRGTMMADALRALRVLPILYQSLSVHLVEINPVLRQKQQTLLAGIRNIHWHDSFEDVPEGPAVILANEYFD
VLPIHQAIKRETGWHERVIEIGASGELVFGVAADPIPGFEALLPPLARLSPPGAVFEWRPDTEILKIASRVRDQGGAALI
IDYGHLRSDVGDTFQAIASHSYADPLQHPGRADLTAHVDFDALGRAAESIGARAHGPVTQGAFLKRLGIETRALSLMAKA
TPQVSEDIAGALQRLTGEGRGAMGSMFKVIGVSDPKIETLVALSDDTDREAERRQGTHGLEHHHHHH


[[Image:1zkd asym r 250.jpg|thumb|1zkd|left]]




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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==
[http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZKD 1zkd]


Located on 2p22.2 on human chromosome with 441 aa
Located on 2p22.2 on human chromosome with 441 aa
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Located on 17E3 on mouse chromosome with 436 aa
Located on 17E3 on mouse chromosome with 436 aa


DUF185 domain identified by Pfam
[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]]


[http://www.rcsb.org/pdb/explore/explore.do?structureId=2EX4 Nearest match - 2ex4]


[http://www.rcsb.org/pdb/explore/explore.do?structureId=1IM8 2nd nearest match - 1im8]
===Pfam Results===


http://cl.sdsc.edu/ce_scratch/ce2162.html
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 


Most probably a transferase as most of the matches from DALI are transferase
                  PdvyartryylvEiSprLaarQketLapkvaplGhdskveieatdlsglv
                  P +y+ ++++lvEi+p L+++Q++ La                ++  ++
      query  106 PILYQSLSVHLVEINPVLRQKQQTLLA-----------------GIR-NI 137 


[http://www.ebi.ac.uk/cgi-bin/iprscan/iprscan?tool=iprscan&jobid=iprscan-20070508-06423459 Interpro Results]
                  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 


===DALI Results===
                  prrksalaaemfngtllqayrqhahddpltnpssllVlyStvaqGlaDiT
                                g+++qa+  h + dpl +p            G+aD+T
      query  250 ------------VGDTFQAIASHSYADPLQHP------------GRADLT 275 


SUMMARY: PDB/chain identifiers and structural alignment statistics
                  ahVDFtalaradqyqtaakaagdlkvlgvet<-*
NR. STRID1 STRID2  Z  RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
                  ahVDF+al      +aa +g + + g+ t    
  1: 3027-A 1zkd-A 56.8  0.0  349  349  100      0      0    1 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    duf185  (rhodops
      query   276 AHVDFDALG------RAAESIG-ARAHGPVT   299
  2: 3027-A 2ex4-A 11.7  3.0  185  221  12      0      0    22 S    TRANSFERASE      adrenal gland protein ad-003    (homo sapien
  3: 3027-A 1im8-A 11.6  3.2  178  225  10      0      0    18 S    TRANSFERASE    yeco (methyltransferase, hypothetical pro
  4: 3027-A 2gb4-A 10.8  3.3  184  231  13      0      0    19 S    TRANSFERASE      thiopurine s-methyltransferase (thiopurine
  5: 3027-A 2fk7-A 10.7  3.8  186  277  14      0      0    19 S    TRANSFERASE      methoxy mycolic acid synthase 4        (mycobact
  6: 3027-A 2ob1-A 10.2 3.9  196   319    9      0      0    23 S    TRANSFERASE      leucine carboxyl methyltransferase 1 (prot
   7: 3027-A 2f8l-A 10.0  3.7  182  318    8      0      0    22 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    hypothetical pro
  8: 3027-A 2avn-A 10.0  3.7  183  242  11      0      0    20 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    ubiquinoneMENAQU
  9: 3027-A 2bzg-A  9.9  3.4  182  226  13      0      0    20 S    TRANSFERASE      thiopurine s-methyltransferase (thiopurine
10: 3027-A 2aot-A  9.8  4.3  182  285  13      0      0    23 S   TRANSFERASE      histamine n-methyltransferase (hmt)    (homo
11: 3027-A 2p8j-A  9.7  3.4  168  203  10      0      0    16 S    TRANSFERASE      s-adenosylmethionine-dependent methyltrans
12: 3027-A 1vl5-A  9.7  3.3  167  225    9      0      0    18 S    STRUCTURAL GENOMICS, UNKNOWN FUNCTION    unknown conserve
13: 3027-A 1hnn-A  9.7  3.4  183  261  13      0      0    18 S    TRANSFERASE    phenylethanolamine n-methyltransferase (p
14: 3027-A 1m6e-X  9.6  3.6  206  359    9      0      0    27 S    TRANSFERASE      s-adenosyl-l-methionnine:salicylic acid ca
15: 3027-A 2fay-A  9.5  3.9  178  274  14      0      0    21 S
16: 3027-A 2h00-A  9.2  2.9  158  225    9      0      0    18 S    TRANSFERASE      methyltransferase 10 domain containing pro
17: 3027-A 1wy7-A  9.2  3.1  155  195  13      0      0    15 S    TRANSFERASE      hypothetical protein ph1948    (pyrococcus h
18: 3027-A 1m6y-A  8.8  4.3  156  289  10      0      0    19 S    TRANSFERASE      s-adenosyl-methyltransferase mraw      (thermo
19: 3027-A 1i9g-A  8.7  3.0  149  264    9      0      0    15 S    TRANSFERASE    hypothetical protein rv2118c    (mycobacter
20: 3027-A 1zq9-A  8.6  3.2  144  278  16      0      0    19 S    TRANSFERASE      probable dimethyladenosine transferase (s-

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
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