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(-) Description

Title :  MOLECULAR BASIS FOR BACTERIAL CLASS 1 RELEASE FACTOR METHYLATION BY PRMC
 
Authors :  M. Graille, V. Heurgue-Hamard, S. Champ, L. Mora, N. Scrima, N. Ulryck, H. Van Tilbeurgh, R. H. Buckingham
Date :  21 Sep 05  (Deposition) - 24 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Release Factor; Translation Termination; Methylation; Conformational Changes (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Graille, V. Heurgue-Hamard, S. Champ, L. Mora, N. Scrima, N. Ulryck, H. Van Tilbeurgh, R. H. Buckingham
Molecular Basis For Bacterial Class I Release Factor Methylation By Prmc
Mol. Cell V. 20 917 2005
PubMed-ID: 16364916  |  Reference-DOI: 10.1016/J.MOLCEL.2005.10.025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN METHYLTRANSFERASE HEMK
    Chains: A
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HEMK
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PROTEIN-GLUTAMINE N- METHYLTRANSFERASE HEMK
 
Molecule 2 - PEPTIDE CHAIN RELEASE FACTOR 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRFA, SUEB, UAR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RF-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:88 , LEU A:89 , PRO A:91 , GLY A:117 , THR A:118 , GLY A:119 , THR A:120 , ALA A:122 , ASP A:140 , ARG A:141 , MET A:142 , SER A:166 , ASP A:167 , TRP A:168 , ASN A:183 , ALA A:206BINDING SITE FOR RESIDUE SAH A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B3T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B3T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B3T)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RF_PROK_IPS00745 Prokaryotic-type class I peptide chain release factors signature.RF1_ECOLI228-244  1B:228-244

(-) Exons   (0, 0)

(no "Exon" information available for 2B3T)

(-) 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:276
 aligned with PRMC_ECOLI | P0ACC1 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:276
                                    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      
           PRMC_ECOLI     1 MEYQHWLREAISQLQASESPRRDAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLTRRRDGEPIAHLTGVREFWSLPLFVSPATLIPRPDTECLVEQALARLPEQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQSDWFSALAGQQFAMIVSNPPYIDEQDPHLQQGDVRFEPLTALVAADSGMADIVHIIEQSRNALVSGGFLLLEHGWQQGEAVRQAFILAGYHDVETCRDYGDNERVTLGRYY 276
               SCOP domains d2b3ta_ A: N5-glutamine methyltransferase, HemK                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------2b3tA02 A:85-276 Vaccinia Virus protein VP39                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhh.eeee..eeee..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...eeee....hhhhh...eeeeee........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..eeeeeeeeee....hhhhhhhhhhhh......eee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b3t A   1 MEYQHWLREAISQLQASESPRRDAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLTRRRDGEPIAHLTGVREFWSLPLFVSPATLIPRPDTECLVEQALARLPEQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQSDWFSALAGQQFAMIVSNPPYIDEQDPHLQQGDVRFEPLTALVAADSGMADIVHIIEQSRNALVSGGFLLLEHGWQQGEAVRQAFILAGYHDVETCRDYGDNERVTLGRYY 276
                                    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      


Chain A from PDB  Type:PROTEIN  Length:276
 aligned with PRMC_SHIFL | P0ACC2 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:276
                                    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      
           PRMC_SHIFL     1 MEYQHWLREAISQLQASESPRRDAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLTRRRDGEPIAHLTGVREFWSLPLFVSPATLIPRPDTECLVEQALARLPEQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQSDWFSALAGQQFAMIVSNPPYIDEQDPHLQQGDVRFEPLTALVAADSGMADIVHIIEQSRNALVSGGFLLLEHGWQQGEAVRQAFILAGYHDVETCRDYGDNERVTLGRYY 276
               SCOP domains d2b3ta_ A: N5-glutamine methyltransferase, HemK                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------2b3tA02 A:85-276 Vaccinia Virus protein VP39                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhh.eeee..eeee..........hhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...eeee....hhhhh...eeeeee........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..eeeeeeeeee....hhhhhhhhhhhh......eee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b3t A   1 MEYQHWLREAISQLQASESPRRDAEILLEHVTGRGRTFILAFGETQLTDEQCQQLDALLTRRRDGEPIAHLTGVREFWSLPLFVSPATLIPRPDTECLVEQALARLPEQPCRILDLGTGTGAIALALASERPDCEIIAVDRMPDAVSLAQRNAQHLAIKNIHILQSDWFSALAGQQFAMIVSNPPYIDEQDPHLQQGDVRFEPLTALVAADSGMADIVHIIEQSRNALVSGGFLLLEHGWQQGEAVRQAFILAGYHDVETCRDYGDNERVTLGRYY 276
                                    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      


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with RF1_ECOLI | P0A7I0 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:348
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346        
            RF1_ECOLI     7 AKLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQEDIETAQMMLDDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQADQLA 354
               SCOP domains ----d2b3tb1 B:7-354 Peptide chain release factor 1,                                    RF1                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..-----------------------------------...........hhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeeeee....hhhhhhhhheeeeeee..........eeeeeeee.................eeeee...............eeeeeee.....eeeeee..hhhhhhhhhhhhhhhhhh........------...-------..eeeeee....eeee.hhheee.hhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RF_PROK_I        -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b3t B   3 AKLEALHERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQV-----------------------------------QQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDVNPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQ------RRN-------SDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQADQLA 354
                                    12        22    ||  36        46        56 |       -         -         -       |96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286|      296       306       316       326       336       346        
                                                   27|                        58                                  94                                                                                                                                                                                              287    294 |     304                                                  
                                                    32                                                                                                                                                                                                                                                                     296
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B3T)

(-) Gene Ontology  (17, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PRMC_SHIFL | P0ACC2)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    GO:0036009    protein-glutamine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamine = S-adenosyl-L-homocysteine + protein N-methyl-L-glutamine.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0018364    peptidyl-glutamine methylation    The addition of a methyl group to a glutamine residue in a protein.
    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.

Chain A   (PRMC_ECOLI | P0ACC1)
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:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    GO:0036009    protein-glutamine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamine = S-adenosyl-L-homocysteine + protein N-methyl-L-glutamine.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0018364    peptidyl-glutamine methylation    The addition of a methyl group to a glutamine residue in a protein.
    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:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).

Chain B   (RF1_ECOLI | P0A7I0)
molecular function
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003747    translation release factor activity    Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
    GO:0016149    translation release factor activity, codon specific    A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PRMC_ECOLI | P0ACC1: 1t43
        RF1_ECOLI | P0A7I0: 1ipn 5j30 5j3c 5j4d

(-) Related Entries Specified in the PDB File

1gqe POLYPEPTIDE CHAIN RELEASE FACTOR 2 (RF2) FROM ESCHERICHIA COLI
1ml5 STRUCTURE OF THE E. COLI RIBOSOMAL TERMINATION COMPLEX WITH RELEASE FACTOR 2
1nv8 N5-GLUTAMINE METHYLTRANSFERASE, HEMK FROM THERMOTOGA MARITIMA
1t43 CRYSTAL STRUCTURE ANALYSIS OF E. COLI PROTEIN (N5)- GLUTAMINE METHYLTRANSFERASE (HEMK)