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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SPOU METHYLTRANSFERASE AVIRB FROM STREPTOMYCES VIRIDOCHROMOGENES IN COMPLEX WITH THE COFACTOR ADOMET
 
Authors :  T. G. Mosbacher, A. Bechthold, G. E. Schulz
Date :  16 Aug 04  (Deposition) - 25 Jan 05  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Spou, C-Terminal Knot, Bound Cofactor Adomet, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. G. Mosbacher, A. Bechthold, G. E. Schulz
Structure And Function Of The Antibiotic Resistance-Mediating Methyltransferase Avirb From Streptomyces Viridochromogenes
J. Mol. Biol. V. 345 535 2005
PubMed-ID: 15581897  |  Reference-DOI: 10.1016/J.JMB.2004.10.051

(-) Compounds

Molecule 1 - RRNA METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX 4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES VIRIDOCHROMOGENES
    Organism Taxid: 1938
    Synonym: AVIRB

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:75 , THR A:210 , ASP A:211 , GLU A:212 , ILE A:231 , GLY A:232 , ASN A:233 , GLU A:234 , THR A:235 , ALA A:236 , GLY A:237 , SER A:251 , ILE A:252 , MET A:254 , LEU A:261 , ALA A:263 , ALA A:266 , HOH A:359 , ARG B:145BINDING SITE FOR RESIDUE SAM A 301
2AC2SOFTWAREARG A:145 , ARG B:79 , THR B:210 , ASP B:211 , GLU B:212 , GLY B:232 , ASN B:233 , GLU B:234 , ALA B:236 , GLY B:237 , SER B:251 , ILE B:252 , MET B:254 , LEU B:261 , ALA B:263 , ALA B:266 , HOH B:322BINDING SITE FOR RESIDUE SAM B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X7P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X7P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X7P)

(-) Exons   (0, 0)

(no "Exon" information available for 1X7P)

(-) 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:265
 aligned with AVRB_STRVR | Q9F5K6 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:265
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277     
           AVRB_STRVR    18 RNARFQQWQALLGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYDGQRELSKWARELLRTVRTEQIAMAPDLLMELGEKNEAPPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRISGR 282
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x7pA01 A:18-118  [code=3.30.1330.30, no name defined]                                               1x7pA02 A:119-282  [code=3.40.1280.10, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhhhhheeeeehhhhhhhhhhh...eeeeeee.....hhhhhhhhhhh..eeeeehhhhhh...........eeeeee....hhhhh......eeeeee...hhhhhhhhhhhhhhh...eeeee.......hhhhhhhh.hhhhh..eeee.hhhhhhhhhhhhhhh....eeeee.....ee.hhh.....eeeee.......hhhhhhhh.eeee..........hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x7p A  18 RNARFQQWQALLGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYDGQRELSKWARELLRTVRTEQIAMAPDLLMELGEKNEAPPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRISGR 282
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277     


Chain B from PDB  Type:PROTEIN  Length:253
 aligned with AVRB_STRVR | Q9F5K6 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:263
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   
           AVRB_STRVR    19 NARFQQWQALLGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYDGQRELSKWARELLRTVRTEQIAMAPDLLMELGEKNEAPPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRISG 281
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1x7pB01 B:19-118  [code=3.30.1330.30, no name d  efined]                                            1x7pB02 B:119-281  [code=3.40.1280.10, no name defined]                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhheeeeehhhhhhhhhhh...eeeeee.--...hhhhhhhhh....eeee..hhhhh--------...eeeeee....hhhhh......eeeeee...hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh....eeeee.....ee.hhh.....eeeee.......hhhhhhhh.eeee..........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x7p B  19 NARFQQWQALLGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYD--RELSKWARELLRTVRTEQIAMAPDLLM--------PPEVVAVVEMPADDLDRIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPMAGSASSLNAANAATAILYEAVRQRISG 281
                                    28        38        48        58      | 68        78        88     |   -    |  108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278   
                                                                         65 68                        94      103
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 1X7P)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1X7P)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (AVRB_STRVR | Q9F5K6)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008650    rRNA (uridine-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methyluridine.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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 Related Entries

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

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        AVRB_STRVR | Q9F5K6: 1x7o

(-) Related Entries Specified in the PDB File

1x7o CRYSTAL STRUCTURE OF THE SPOU METHYLTRANSFERASE AVIRB FROM STREPTOMYCES VIRIDOCHROMOGENES