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(-) Description

Title :  STRUCTURE OF THE PREDOMINANT PROTEIN ARGININE METHYLTRANSFERASE PRMT1
 
Authors :  X. Zhang, X. Cheng
Date :  13 Mar 03  (Deposition) - 27 May 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Protein Arginine Methylation Adomet-Dependent Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Zhang, X. Cheng
Structure Of The Predominant Protein Arginine Methyltransferase Prmt1 And Analysis Of Its Binding To Substrate Peptides
Structure V. 11 509 2003
PubMed-ID: 12737817  |  Reference-DOI: 10.1016/S0969-2126(03)00071-6

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 1
    ChainsA
    EC Number2.1.1.125
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentM11
    GeneHRMT1L2 OR PRMT1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:45 , MET A:48 , ARG A:54 , GLY A:78 , GLY A:80 , ILE A:83 , GLU A:100 , CYS A:101 , SER A:102 , GLY A:126 , LYS A:127 , VAL A:128 , GLU A:144 , MET A:155 , HOH A:372 , HOH A:373 , HOH A:374 , UNL A:700BINDING SITE FOR RESIDUE SAH A 354
2AC2SOFTWAREARG A:177 , THR A:179 , TYR A:181 , ASN A:271 , GLU A:273BINDING SITE FOR RESIDUE UNL A 355
3AC3SOFTWAREMET A:48 , GLU A:144 , MET A:146 , SAH A:354BINDING SITE FOR RESIDUE UNL A 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:174 -Pro A:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ORI)

(-) 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:316
 aligned with ANM1_RAT | Q63009 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:316
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347      
             ANM1_RAT    38 SYAHFGIHEEMLKDEVRTLTYRNSMFHNRHLFKDKVVLDVGSGTGILCMFAAKAGARKVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDIIISEWMGYCLFYESMLNTVLHARDKWLAPDGLIFPDRATLYVTAIEDRQYKDYKIHWWENVYGFDMSCIKDVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVHALVAYFNIEFTRCHKRTGFSTSPESPYTHWKQTVFYMEDYLTVKTGEEIFGTIGMRPNAKNNRDLDFTIDLDFKGQLCELSCSTDYRMR 353
               SCOP domains d1oria_ A: Protein arginine N-methyltransferase 1, PRMT1                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1oriA01 A:38-175 Vaccinia Virus protein VP39                                                                                              -1oriA02 A:177-353 Hnrnp arginine n-methyltransferase1                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeeee............eeeeee...........hhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhh..........hhhhhhhhhh..eee..hhh.eeeeeeeeeeee....hhhhhheeeeeeee....eeeeeeeeeeeee........eee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ori A  38 SYAHFGIHEEMLKDEVRTLTYRNSMFHNRHLFKDKVVLDVGSGTGILCMFAAKAGARKVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVDIIISEWMGYCLFYESMLNTVLHARDKWLAPDGLIFPDRATLYVTAIEDRQYKDYKIHWWENVYGFDMSCIKDVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVHALVAYFNIEFTRCHKRTGFSTSPESPYTHWKQTVFYMEDYLTVKTGEEIFGTIGMRPNAKNNRDLDFTIDLDFKGQLCELSCSTDYRMR 353
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347      

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ORI)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A   (ANM1_RAT | Q63009)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0016275    [cytochrome c]-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (cytochrome c)-arginine = S-adenosyl-L-homocysteine + (cytochrome c)-N(omega)-methyl-arginine.
    GO:0044020    histone methyltransferase activity (H4-R3 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + (histone H4)-arginine (position 3) = S-adenosyl-L-homocysteine + (histone H4)-N-methyl-arginine (position 3). This reaction is the addition of a methyl group to arginine at position 3 of histone H4.
    GO:0008469    histone-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008327    methyl-CpG binding    Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    GO:0016274    protein-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine.
    GO:0035242    protein-arginine omega-N asymmetric methyltransferase activity    Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues.
    GO:0035241    protein-arginine omega-N monomethyltransferase activity    Catalysis of the addition of a methyl group to either of the unmethylated terminal nitrogen atoms (also called omega nitrogen) in peptidyl-arginine to form an omega-N-G-monomethylated arginine residue. The reaction is S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-Nomega-methyl-L-arginine.
    GO:0030519    snoRNP binding    Interacting selectively and non-covalently with any part of a small nucleolar ribonucleoprotein particle.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0043985    histone H4-R3 methylation    The modification of histone H4 by addition of a methyl group to arginine at position 3 of the histone.
    GO:0097421    liver regeneration    The regrowth of lost or destroyed liver.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0045653    negative regulation of megakaryocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
    GO:0018216    peptidyl-arginine methylation    The addition of a methyl group to an arginine residue in a protein.
    GO:0019919    peptidyl-arginine methylation, to asymmetrical-dimethyl arginine    The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N(omega)-dimethyl-L-arginine.
    GO:0035247    peptidyl-arginine omega-N-methylation    The addition of a methyl group onto a terminal nitrogen (omega nitrogen) atom of an arginine residue in a protein.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0046985    positive regulation of hemoglobin biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin.
    GO:1900745    positive regulation of p38MAPK cascade    Any process that activates or increases the frequency, rate or extent of p38MAPK cascade.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0034709    methylosome    A large (20 S) protein complex that possesses protein arginine methyltransferase activity and modifies specific arginines to dimethylarginines in the arginine- and glycine-rich domains of several spliceosomal Sm proteins, thereby targeting these proteins to the survival of motor neurons (SMN) complex for assembly into small nuclear ribonucleoprotein (snRNP) core particles. Proteins found in the methylosome include the methyltransferase JBP1 (PRMT5), pICln (CLNS1A), MEP50 (WDR77), and unmethylated forms of SM proteins that have RG domains.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ANM1_RAT | Q630091or8 1orh 3q7e

(-) Related Entries Specified in the PDB File

1f3l BINARY STRUCTURE OF PRMT3
1or8 TERNARY STRUCUTRE OF PRMT1
1orh TERNARY STRUCTURE OF MUTANT PRMT1 (E153Q)