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(-) Description

Title :  CRYSTAL STRUCTURE OF PH1915 (APC 5817): A HYPOTHETICAL RNA METHYLTRANSFERASE
 
Authors :  W. Sun, X. Xu, M. Pavlova, A. M. Edwards, A. Joachimiak, A. Savchenko, D. Christendat, Midwest Center For Structural Genomics (Mcsg)
Date :  22 Aug 05  (Deposition) - 20 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Methyltransferase, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Sun, X. Xu, M. Pavlova, A. M. Edwards, A. Joachimiak, A. Savchenko, D. Christendat
The Crystal Structure Of A Novel Sam-Dependent Methyltransferase Ph1915 From Pyrococcus Horikoshii.
Protein Sci. V. 14 3121 2005
PubMed-ID: 16260766  |  Reference-DOI: 10.1110/PS.051821805
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH1915
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: P11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PH1915
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 28)

Asymmetric/Biological Unit (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2AS0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AS0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AS0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AS0)

(-) Exons   (0, 0)

(no "Exon" information available for 2AS0)

(-) Sequences/Alignments

Asymmetric/Biological 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:396
 aligned with O59578_PYRHO | O59578 from UniProtKB/TrEMBL  Length:396

    Alignment length:396
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390      
         O59578_PYRHO     1 MARVVVDAQAARAIGKGAMIVFKKGVVRVEGDIKPGDIVEVYTRGGKFLGKGFANPNSNIMVRIVTKDKDVEINKDLFKRRIKKANEYRKKVLKYTNVYRMVYGEADYLPGLIVDRFNDIASLQISSAGMERFKLDVAEAIMEVEPGIETVFEKNTGRSRRREGLPEIERVLLGKEKYRTIIQEGRAKFIVDMRGQKTGFFLDQRENRLALEKWVQPGDRVLDVFTYTGGFAIHAAIAGADEVIGIDKSPRAIETAKENAKLNGVEDRMKFIVGSAFEEMEKLQKKGEKFDIVVLDPPAFVQHEKDLKAGLRAYFNVNFAGLNLVKDGGILVTCSCSQHVDLQMFKDMIIAAGAKAGKFLKMLEPYRTQAPDHPILMASKDTEYLKCLFLYVEDMR 396
               SCOP domains d2as0a1 A:1-72 Hypothetical protein PH1915, N-terminal domain           d2as0a2 A:73-396 Hypothetical protein PH1915, middle and C-terminal domains                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -2as0A01 A:2-71  [code=2.30.130.10, no name defined]                   2as0A02 A:72-178 RNA methyltransferase domain (HRMD) like                                                  2as0A03 A:179-396 Vaccinia Virus protein VP39                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhh...eee...eeeee.......eeeeee....eeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhh....eeeeeee....eeeeee..eeeeee...........hhhhhhhhhhhh....eeee.....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhh.eeeee................hhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2as0 A   1 mARVVVDAQAARAIGKGAmIVFKKGVVRVEGDIKPGDIVEVYTRGGKFLGKGFANPNSNImVRIVTKDKDVEINKDLFKRRIKKANEYRKKVLKYTNVYRmVYGEADYLPGLIVDRFNDIASLQISSAGmERFKLDVAEAImEVEPGIETVFEKNTGRSRRREGLPEIERVLLGKEKYRTIIQEGRAKFIVDmRGQKTGFFLDQRENRLALEKWVQPGDRVLDVFTYTGGFAIHAAIAGADEVIGIDKSPRAIETAKENAKLNGVEDRmKFIVGSAFEEmEKLQKKGEKFDIVVLDPPAFVQHEKDLKAGLRAYFNVNFAGLNLVKDGGILVTCSCSQHVDLQmFKDmIIAAGAKAGKFLKmLEPYRTQAPDHPILmASKDTEYLKCLFLYVEDmR 396
                            |       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       260       270       280       290       300       310       320       330       340   |   350       360 |     370      |380       390    | 
                            |                19-MSE                                    61-MSE                                 101-MSE                      130-MSE     142-MSE                                            193-MSE                                                                     269-MSE    280-MSE                                                         344-MSE           362-MSE        377-MSE           395-MSE
                            1-MSE                                                                                                                                                                                                                                                                                                                                                    348-MSE                                            


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with O59578_PYRHO | O59578 from UniProtKB/TrEMBL  Length:396

    Alignment length:396
                                    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       260       270       280       290       300       310       320       330       340       350       360       370       380       390      
         O59578_PYRHO     1 MARVVVDAQAARAIGKGAMIVFKKGVVRVEGDIKPGDIVEVYTRGGKFLGKGFANPNSNIMVRIVTKDKDVEINKDLFKRRIKKANEYRKKVLKYTNVYRMVYGEADYLPGLIVDRFNDIASLQISSAGMERFKLDVAEAIMEVEPGIETVFEKNTGRSRRREGLPEIERVLLGKEKYRTIIQEGRAKFIVDMRGQKTGFFLDQRENRLALEKWVQPGDRVLDVFTYTGGFAIHAAIAGADEVIGIDKSPRAIETAKENAKLNGVEDRMKFIVGSAFEEMEKLQKKGEKFDIVVLDPPAFVQHEKDLKAGLRAYFNVNFAGLNLVKDGGILVTCSCSQHVDLQMFKDMIIAAGAKAGKFLKMLEPYRTQAPDHPILMASKDTEYLKCLFLYVEDMR 396
               SCOP domains d2as0b1 B:1-72 Hypothetical protein PH1915, N-terminal domain           d2as0b2 B:73-396 Hypothetical protein PH1915, middle and C-terminal domains                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -2as0B01 B:2-71  [code=2.30.130.10, no name defined]                   2as0B02 B:72-178 RNA methyltransferase domain (HRMD) like                                                  2as0B03 B:179-396 Vaccinia Virus protein VP39                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhh...eee...eeeee.......eeeeee....eeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhhhhh.....eeeeee.hhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhh.....eeeeeee....eeeeee..eeeeee........hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhheeeee................hhhhh..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2as0 B   1 mARVVVDAQAARAIGKGAmIVFKKGVVRVEGDIKPGDIVEVYTRGGKFLGKGFANPNSNImVRIVTKDKDVEINKDLFKRRIKKANEYRKKVLKYTNVYRmVYGEADYLPGLIVDRFNDIASLQISSAGmERFKLDVAEAImEVEPGIETVFEKNTGRSRRREGLPEIERVLLGKEKYRTIIQEGRAKFIVDmRGQKTGFFLDQRENRLALEKWVQPGDRVLDVFTYTGGFAIHAAIAGADEVIGIDKSPRAIETAKENAKLNGVEDRmKFIVGSAFEEmEKLQKKGEKFDIVVLDPPAFVQHEKDLKAGLRAYFNVNFAGLNLVKDGGILVTCSCSQHVDLQmFKDmIIAAGAKAGKFLKmLEPYRTQAPDHPILmASKDTEYLKCLFLYVEDmR 396
                            |       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       260       270       280       290       300       310       320       330       340   |   350       360 |     370      |380       390    | 
                            |                19-MSE                                    61-MSE                                 101-MSE                      130-MSE     142-MSE                                            193-MSE                                                                     269-MSE    280-MSE                                                         344-MSE           362-MSE        377-MSE           395-MSE
                            1-MSE                                                                                                                                                                                                                                                                                                                                                    348-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AS0)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O59578_PYRHO | O59578)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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