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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SAM-DEPENDENT METHYLTRANSFERASE FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  H. Mizutani, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Mar 05  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Sam-Dependent Methyltransferase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, N. Kunishima
Crystal Structure Of The Sam-Dependent Methyltransferase From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SAM-DEPENDENT METHYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: 252AA LONG HYPOTHETICAL PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2SAH3Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SAH6Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO46Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:77 , ARG A:81 , HOH A:1035 , HOH A:1132 , HOH A:1229BINDING SITE FOR RESIDUE SO4 A 1004
2AC2SOFTWAREARG B:77 , ARG B:81 , HOH B:1023 , HOH B:1082 , HOH B:1192BINDING SITE FOR RESIDUE SO4 B 1005
3AC3SOFTWAREARG C:77 , ARG C:81 , HOH C:1034 , HOH C:1125 , HOH C:1132BINDING SITE FOR RESIDUE SO4 C 1006
4AC4SOFTWAREASP A:120 , HOH A:1062 , HOH A:1181BINDING SITE FOR RESIDUE MG A 1007
5AC5SOFTWARETYR A:5 , TYR A:12 , ARG A:19 , ALA A:49 , CYS A:50 , GLY A:51 , PRO A:55 , ASP A:70 , LEU A:71 , HIS A:72 , MET A:75 , GLY A:95 , ASP A:96 , VAL A:97 , PHE A:112 , PHE A:113 , THR A:115 , PHE A:119 , HOH A:1008 , HOH A:1009 , HOH A:1010 , HOH A:1060BINDING SITE FOR RESIDUE SAH A 1001
6AC6SOFTWARETYR B:5 , TYR B:12 , ARG B:19 , ALA B:49 , CYS B:50 , GLY B:51 , PRO B:55 , ASP B:70 , LEU B:71 , HIS B:72 , MET B:75 , GLY B:95 , ASP B:96 , VAL B:97 , PHE B:112 , PHE B:113 , THR B:115 , PHE B:119 , HOH B:1006 , HOH B:1008 , HOH B:1013 , HOH B:1094 , HOH B:1098BINDING SITE FOR RESIDUE SAH B 1002
7AC7SOFTWARETYR C:5 , TYR C:12 , ARG C:19 , ALA C:49 , CYS C:50 , GLY C:51 , PRO C:55 , ASP C:70 , LEU C:71 , HIS C:72 , MET C:75 , GLY C:95 , ASP C:96 , VAL C:97 , PHE C:112 , PHE C:113 , THR C:115 , PHE C:119 , HOH C:1007 , HOH C:1008 , HOH C:1023 , HOH C:1049 , HOH C:1105BINDING SITE FOR RESIDUE SAH C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WZN)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly C:155 -Pro C:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WZN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WZN)

(-) Exons   (0, 0)

(no "Exon" information available for 1WZN)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:244
 aligned with O59000_PYRHO | O59000 from UniProtKB/TrEMBL  Length:252

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
         O59000_PYRHO     1 MYELYTLLAEYYDTIYRRRIERVKAEIDFVEEIFKEDAKREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDAVTMFFSTIMYFDEEDLRKLFSKVAEALKPGGVFITDFPCWFYGGRDGPVVWNEQKGEEKLVIMDWREVEPAVQKLRFKRLVQILRPNGEVKAFLVDDELNIYTPREVRLLAEKYFEKVKIYGNLKRELSPNDMRYWIVGIAKS 251
               SCOP domains d1wzna1 A:1-251 Hypothetical methyltransferase PH1305                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.-------..eeeeeee..eeeeeeeeeeee....eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhh....eeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wzn A   1 MYELYTLLAEYYDTIYRRRIERVKAEIDFVEEIFKEDAKREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDAVTMFFSTIMYFDEEDLRKLFSKVAEALKPGGVFITDFPC-------GPVVWNEQKGEEKLVIMDWREVEPAVQKLRFKRLVQILRPNGEVKAFLVDDELNIYTPREVRLLAEKYFEKVKIYGNLKRELSPNDMRYWIVGIAKS 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |  -    |  160       170       180       190       200       210       220       230       240       250 
                                                                                                                                                                            147     155                                                                                                


Chain B from PDB  Type:PROTEIN  Length:244
 aligned with O59000_PYRHO | O59000 from UniProtKB/TrEMBL  Length:252

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
         O59000_PYRHO     1 MYELYTLLAEYYDTIYRRRIERVKAEIDFVEEIFKEDAKREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDAVTMFFSTIMYFDEEDLRKLFSKVAEALKPGGVFITDFPCWFYGGRDGPVVWNEQKGEEKLVIMDWREVEPAVQKLRFKRLVQILRPNGEVKAFLVDDELNIYTPREVRLLAEKYFEKVKIYGNLKRELSPNDMRYWIVGIAKS 251
               SCOP domains d1wznb_ B: Hypothetical methyltransferase PH1305                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.-------..eeeeeee..eeeeeeeeeeee....eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhhh...eeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wzn B   1 MYELYTLLAEYYDTIYRRRIERVKAEIDFVEEIFKEDAKREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDAVTMFFSTIMYFDEEDLRKLFSKVAEALKPGGVFITDFPC-------GPVVWNEQKGEEKLVIMDWREVEPAVQKLRFKRLVQILRPNGEVKAFLVDDELNIYTPREVRLLAEKYFEKVKIYGNLKRELSPNDMRYWIVGIAKS 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |  -    |  160       170       180       190       200       210       220       230       240       250 
                                                                                                                                                                            147     155                                                                                                


Chain C from PDB  Type:PROTEIN  Length:244
 aligned with O59000_PYRHO | O59000 from UniProtKB/TrEMBL  Length:252

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
         O59000_PYRHO     1 MYELYTLLAEYYDTIYRRRIERVKAEIDFVEEIFKEDAKREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDAVTMFFSTIMYFDEEDLRKLFSKVAEALKPGGVFITDFPCWFYGGRDGPVVWNEQKGEEKLVIMDWREVEPAVQKLRFKRLVQILRPNGEVKAFLVDDELNIYTPREVRLLAEKYFEKVKIYGNLKRELSPNDMRYWIVGIAKS 251
               SCOP domains d1wznc_ C: Hypothetical methyltransferase PH1305                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------Methyltransf_18-1wznC01 C:41-146                                                                          --------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------Methyltransf_18-1wznC02 C:41-146                                                                          --------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------Methyltransf_18-1wznC03 C:41-146                                                                          --------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.-------..eeeeeee..eeeeeeeeeeee....eeeeeeeeeee.....eeeeeeeeeee..hhhhhhhhhh....eeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wzn C   1 MYELYTLLAEYYDTIYRRRIERVKAEIDFVEEIFKEDAKREVRRVLDLACGTGIPTLELAERGYEVVGLDLHEEMLRVARRKAKERNLKIEFLQGDVLEIAFKNEFDAVTMFFSTIMYFDEEDLRKLFSKVAEALKPGGVFITDFPC-------GPVVWNEQKGEEKLVIMDWREVEPAVQKLRFKRLVQILRPNGEVKAFLVDDELNIYTPREVRLLAEKYFEKVKIYGNLKRELSPNDMRYWIVGIAKS 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |  -    |  160       170       180       190       200       210       220       230       240       250 
                                                                                                                                                                            147     155
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WZN)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1WZN)

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