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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE RUMA IN COMPLEX WITH RIBOSOMAL RNA SUBSTRATE AND S-ADENOSYLHOMOCYSTEINE.
 
Authors :  T. T. Lee, S. Agarwalla, R. M. Stroud
Date :  06 Jan 05  (Deposition) - 30 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Iron-Sulfur Cluster, Methyltransferase, Rna Modification, Rna Processing, Transferase, Ruma, Base Flipping, Sam, Ob- Fold, Protein-Rna Complex, Base Stacking, Substrate Selectivity, General Base, Product Release, 4Fe-4S, Direct Protein Sequencing, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. T. Lee, S. Agarwalla, R. M. Stroud
A Unique Rna Fold In The Ruma-Rna-Cofactor Ternary Complex Contributes To Substrate Selectivity And Enzymatic Function
Cell(Cambridge, Mass. ) V. 120 599 2005
PubMed-ID: 15766524  |  Reference-DOI: 10.1016/J.CELL.2004.12.037
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
    ChainsA, B
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET15B
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsIRON-SULFUR CLUSTER LINKED BY CYS81, CYS87, CYS90, AND CYS162
    StrainK12
    Synonym23S RRNA(M-5-U1939)-METHYLTRANSFERASE, 23S RRNA URACIL-5-METHYLTRANSFERASE RUMA
 
Molecule 2 - 23S RIBOSOMAL RNA 1932-1968
    ChainsC, D
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other Details5-FLUORO-U1939 IS METHYLATED AND ITS 6-C IS COVALENTLY LINKED TO CYS389 OF RUMA
    StrainK12
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1FMU2Mod. Nucleotide5-FLUORO-5-METHYLURIDINE-5'-MONOPHOSPHATE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1FMU1Mod. Nucleotide5-FLUORO-5-METHYLURIDINE-5'-MONOPHOSPHATE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1FMU1Mod. Nucleotide5-FLUORO-5-METHYLURIDINE-5'-MONOPHOSPHATE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:263 , GLN A:265 , PHE A:294 , CYS A:295 , ASN A:299 , PHE A:300 , GLU A:315 , GLY A:316 , VAL A:317 , LEU A:320 , GLU A:341 , ASN A:342 , LEU A:343 , GLU A:344 , ASP A:363 , HOH A:2112 , HOH A:2133 , HOH A:2134 , HOH A:2135 , A C:1937 , FMU C:1939BINDING SITE FOR RESIDUE SAH A 500
2AC2SOFTWARECYS A:81 , CYS A:87 , CYS A:90 , GLN A:93 , GLN A:161 , CYS A:162 , PRO A:163 , ILE A:164 , U C:1940BINDING SITE FOR RESIDUE SF4 A 501
3AC3SOFTWAREPHE B:263 , GLN B:265 , PHE B:294 , CYS B:295 , MET B:297 , ASN B:299 , GLU B:315 , GLY B:316 , VAL B:317 , LEU B:320 , GLU B:341 , ASN B:342 , LEU B:343 , ASP B:363 , HOH B:2088 , HOH B:2129 , HOH B:2130 , HOH B:2131 , A D:1937 , FMU D:1939BINDING SITE FOR RESIDUE SAH B 500
4AC4SOFTWARECYS B:81 , CYS B:87 , CYS B:90 , GLN B:93 , GLN B:161 , CYS B:162 , PRO B:163BINDING SITE FOR RESIDUE SF4 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BH2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BH2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BH2)

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_RNA_M5UPS51687 SAM-dependent methyltransferase RNA m(5)U-type domain profile.RLMD_ECOLI88-432
 
  2A:88-432
B:88-431
2TRMA_1PS01230 RNA methyltransferase trmA family signature 1.RLMD_ECOLI363-393
 
  2A:363-393
B:363-393
3TRMA_2PS01231 RNA methyltransferase trmA family signature 2.RLMD_ECOLI414-424
 
  2A:414-424
B:414-424
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_RNA_M5UPS51687 SAM-dependent methyltransferase RNA m(5)U-type domain profile.RLMD_ECOLI88-432
 
  1A:88-432
-
2TRMA_1PS01230 RNA methyltransferase trmA family signature 1.RLMD_ECOLI363-393
 
  1A:363-393
-
3TRMA_2PS01231 RNA methyltransferase trmA family signature 2.RLMD_ECOLI414-424
 
  1A:414-424
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_RNA_M5UPS51687 SAM-dependent methyltransferase RNA m(5)U-type domain profile.RLMD_ECOLI88-432
 
  1-
B:88-431
2TRMA_1PS01230 RNA methyltransferase trmA family signature 1.RLMD_ECOLI363-393
 
  1-
B:363-393
3TRMA_2PS01231 RNA methyltransferase trmA family signature 2.RLMD_ECOLI414-424
 
  1-
B:414-424

(-) Exons   (0, 0)

(no "Exon" information available for 2BH2)

(-) 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:418
 aligned with RLMD_ECOLI | P55135 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:418
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        
          RLMD_ECOLI     15 QIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSADREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAMLDMFPHTGHLESMVLFSRV  432
               SCOP domains d2bh2a1 A:15-74                                             d2bh2a2 A:75-432 rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.ee.....eeeee..eeeee......eeeeeee......eeeeeeeee..........................hhhhhhhhhhhhhhhhhh....eee.........eeeeeeeee....eeeeeee......eee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhh.eeeeee......ee......eeee..eeee.........hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhh...eeee.........hhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.eeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------SAM_MT_RNA_M5U  PDB: A:88-432 UniProt: 88-432                                                                                                                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRMA_1  PDB: A:363-393         --------------------TRMA_2     -------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bh2 A   15 QIITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSADREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAMLDMFPHTGHLESMVLFSRV  432
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        

Chain B from PDB  Type:PROTEIN  Length:416
 aligned with RLMD_ECOLI | P55135 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:416
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425      
          RLMD_ECOLI     16 IITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSADREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAMLDMFPHTGHLESMVLFSR  431
               SCOP domains d2bh2b1 B:16-74                                            d2bh2b2 B:75-431 rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..ee.....eeeee..eeeee.......eeeeeeeee...eeeeeeeee..........................hhhhhhhhhhhhhhhhhh....eee.........eeeeeeee......eeeeee......eee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhh..eeeeeee..eeeeee....eeee..eeee.........hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.....hhhhhhhhh....eeee......hhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh...eeeeeeee.........eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------SAM_MT_RNA_M5U  PDB: B:88-431 UniProt: 88-432                                                                                                                                                                                                                                                                                                            PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRMA_1  PDB: B:363-393         --------------------TRMA_2     ------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2bh2 B   16 IITVSVNDLDSFGQGVARHNGKTLFIPGLLPQENAEVTVTEDKKQYARAKVVRRLSDSPERETPRCPHFGVCGGCQQQHASVDLQQRSKSAALARLMKHDVSEVIADVPWGYRRRARLSLNYLPKTQQLQMGFRKAGSSDIVDVKQCPILAPQLEALLPKVRACLGSLQAMRHLGHVELVQATSGTLMILRHTAPLSSADREKLERFSHSEGLDLYLAPDSEILETVSGEMPWYDSNGLRLTFSPRDFIQVNAGVNQKMVARALEWLDVQPEDRVLDLFCGMGNFTLPLATQAASVVGVEGVPALVEKGQQNARLNGLQNVTFYHENLEEDVTKQPWAKNGFDKVLLDPARAGAAGVMQQIIKLEPIRIVYVSCNPATLARDSEALLKAGYTIARLAMLDMFPHTGHLESMVLFSR  431
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425      

Chain C from PDB  Type:RNA  Length:30
                                                               
                2bh2 C 1932 AGCGAAAuUCCUUGUCGGGUAAGUUCCGAC 1961
                                  1941      1951      1961
                                1939-FMU                  

Chain D from PDB  Type:RNA  Length:30
                                                               
                2bh2 D 1932 AGCGAAAuUCCUUGUCGGGUAAGUUCCGAC 1961
                                  1941      1951      1961
                                1939-FMU                  

   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 Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BH2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BH2)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RLMD_ECOLI | P55135)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0070041    rRNA (uridine-C5-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C5-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:0070475    rRNA base methylation    The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

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 Related Entries

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

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        RLMD_ECOLI | P551351uwv

(-) Related Entries Specified in the PDB File

1uwv CRYSTAL STRUCTURE OF RUMA, THE IRON-SULFUR CLUSTER CONTAINING E. COLI 23S RIBOSOMAL RNA 5-METHYLURIDINE METHYLTRANSFERASE