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

Authors :   T. T. Lee, S. Agarwalla, R. M. Stroud

Date :   11 Feb 04 (Deposition) - 18 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A

Keywords :   Methyltransferase, Rna Modification, Iron-Sulfur Cluster, Transferase, Rna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. T. Lee, S. Agarwalla, R. M. Stroud
Crystal Structure Of Ruma, An Iron-Sulfur Cluster Containing E. Coli Ribosomal Rna 5-Methyluridine Methyltransferase.
Structure V. 12 397 2004
PubMed-ID: 15016356 | Reference-DOI: 10.1016/J.STR.2004.02.009
(for further references see the PDB file header)

Molecule 1 - 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
	Chains	:	A
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	IRON-SULFUR CLUSTER LINKED BY CYS81, CYS87, CYS90, AND CYS162
	Strain	:	K12
	Synonym	:	23S RRNA(M-5-U1939)-METHYLTRANSFERASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 16)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
3	NI	2	Ligand/Ion	NICKEL (II) ION
4	PO4	1	Ligand/Ion	PHOSPHATE ION
5	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	NI A:1434	BINDING SITE FOR RESIDUE CL A1436
2	AC2	SOFTWARE	CYS A:81 , CYS A:87 , CYS A:90 , GLN A:93 , GLN A:161 , CYS A:162 , PRO A:163 , ILE A:164	BINDING SITE FOR RESIDUE SF4 A1432
3	AC3	SOFTWARE	HIS A:114 , ILE A:408 , HOH A:2050 , HOH A:2116 , HOH A:2117	BINDING SITE FOR RESIDUE NI A1433
4	AC4	SOFTWARE	ARG A:132 , HIS A:191 , GLU A:193 , CL A:1436	BINDING SITE FOR RESIDUE NI A1434
5	AC5	SOFTWARE	ARG A:132 , HIS A:191 , ARG A:206 , SER A:236 , LYS A:273	BINDING SITE FOR RESIDUE PO4 A1435

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

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

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_RNA_M5U	PS51687	SAM-dependent methyltransferase RNA m(5)U-type domain profile.	RLMD_ECOLI	88-432	1	A:88-432
2	TRMA_1	PS01230	RNA methyltransferase trmA family signature 1.	RLMD_ECOLI	363-393	1	A:363-393
3	TRMA_2	PS01231	RNA methyltransferase trmA family signature 2.	RLMD_ECOLI	414-424	1	A:414-424

(no "Exon" information available for 1UWV)

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
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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 d1uwva1 A:15-74                                             d1uwva2 A:75-432 rRNA (Uracil-5-)-methyltransferase RumA, catalytic domain                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeee..eeeeee......eeeeeeeee...eeeeeeeee..........................hhhhhhhhhhhhhhhhhh....eee.........eeeeeeeee....eeeeeee......eee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhh.eeeee......eeee....eeee..eeee.........hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.........hhhhh....eeee......hhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh..eeeeeeee.........eeeeeee.. 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
                 1uwv 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 |      
                                                                                                                           112-MSE                           146-MSE                                 186-MSE          203-MSE                                    246-MSE                     274-MSE                297-MSE                                                                     373-MSE                                 413-MSE      426-MSE  
                                                                                                                                                                                                                                                                                                                                                                                                                                           416-MSE

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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 '\|'

(no "CATH Domain" information available for 1UWV)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (5, 16)

Sites (5, 5)

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