2ERC - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ERMC' A RRNA-METHYL TRANSFERASE

Authors :   D. E. Bussiere, S. W. Muchmore, C. G. Dealwis, G. Schluckebier, C. Abad- Zapatero

Date :   13 Mar 98 (Deposition) - 23 Mar 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.03

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Methyltransferase, Antibiotic Resistance, Rrna Methyltransferase, Erythromycin Resistance Methylase C' (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. E. Bussiere, S. W. Muchmore, C. G. Dealwis, G. Schluckebier, V. L. Nienaber, R. P. Edalji, K. A. Walter, U. S. Ladror, T. F. Holzman, C. Abad-Zapatero
Crystal Structure Of Ermc', An Rrna Methyltransferase Which Mediates Antibiotic Resistance In Bacteria.
Biochemistry V. 37 7103 1998
PubMed-ID: 9585521 | Reference-DOI: 10.1021/BI973113C
(for further references see the PDB file header)

Molecule 1 - RRNA METHYL TRANSFERASE
	Cell Line	:	B834
	Chains	:	A, B
	EC Number	:	2.1.1.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	ERMC'
	Expression System Plasmid	:	PTERM31
	Expression System Strain	:	BL219 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector	:	PTERM
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 10-244
	Gene	:	ERMC'
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	BD1109
	Synonym	:	ERMC'
	Variant	:	ERMC'

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2ERC)

(no "Site" information available for 2ERC)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	ERM_BACIU	34-61	2	A:34-61 B:34-61

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	ERM_BACIU	34-61	1	A:34-61 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	ERM_BACIU	34-61	1	- B:34-61

(no "Exon" information available for 2ERC)

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:235
 aligned with ERM_BACIU | P13956 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
            ERM_BACIU    10 QNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK 244
               SCOP domains d2erca_ A: rRNA adenine dimethylase                                                                                                                                                                                                         SCOP domains
               CATH domains 2ercA01 A:10-134,A:149-180 Vaccinia Virus protein VP39                                                                       2ercA02       2ercA01 A:10-134,A:149-180      2ercA02 A:135-148,A:181-244  [code=1.10.8.100, no name defined]  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhh........eee......hhhhhhh.....eee....hhhhhhhhhh.............hhh.........eeee........hhhhhhhh.....eeeeeeehhhhhhhh....hhhhhhhh.eeeee................eeeeeeee.......hhhhhhhhhhhhhh.........hhhhhhhhhh...........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: A:34-61 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2erc A  10 QNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK 244
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with ERM_BACIU | P13956 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
            ERM_BACIU    10 QNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK 244
               SCOP domains d2ercb_ B: rRNA adenine dimethylase                                                                                                                                                                                                         SCOP domains
               CATH domains 2ercB01 B:10-134,B:149-180 Vaccinia Virus protein VP39                                                                       2ercB02       2ercB01 B:10-134,B:149-180      2ercB02 B:135-148,B:181-244  [code=1.10.8.100, no name defined]  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhh.hhh........eee......hhhhhhh.....eee....hhhhhhhhhh.............hhh.........eeee.......hhhhhhhhh.....eeeeeeehhhhhhhh....hhhhhhhh.eeeee................eeeeeeee......hhh.hhhhhhhhhhh.........hhhhhhhhhh...........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: B:34-61 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2erc B  10 QNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK 244
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

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 '\|'

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (ERM_BACIU | P13956)

molecular function
	GO:0052910	23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity	Catalysis of the reaction: 2 S-adenosyl-L-methionine + adenine(2085) in 23S rRNA = 2 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(2085) in 23S rRNA.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0000179	rRNA (adenine-N6,N6-)-dimethyltransferase activity	Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
	GO:0008649	rRNA methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
	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:0031167	rRNA methylation	The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
	GO:0000154	rRNA modification	The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
	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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2erc)

	Sites
(no "Sites" information available for 2erc)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2erc)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2erc
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ERM_BACIU \| P13956
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.1.1.48
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ERM_BACIU \| P13956
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ERM_BACIU \| P13956	:	1qam 1qan 1qao 1qaq

(no "Related Entries Specified in the PDB File" available for 2ERC)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File