1P91 - JenaLib

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Title :   CRYSTAL STRUCTURE OF RLMA(I) ENZYME: 23S RRNA N1-G745 METHYLTRANSFERASE (NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER19)

Authors :   K. Das, T. Acton, G. Montelione, E. Arnold, Northeast Structural Genomics Consortium (Nesg)

Date :   08 May 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Rlma, Rrma, Methyltransferase, G745, Er19, 23S Rrna, Nesg, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Das, T. Acton, Y. Chiang, L. Shih, E. Arnold, G. T. Montelione
Crystal Structure Of Rlmai: Implications For Understanding The 23S Rrna G745/G748-Methylation At The Macrolide Antibiotic-Binding Site.
Proc. Natl. Acad. Sci. Usa V. 101 4041 2004
PubMed-ID: 14999102 | Reference-DOI: 10.1073/PNAS.0400189101
(for further references see the PDB file header)

Molecule 1 - RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE A
	Chains	:	A, B
	EC Number	:	2.1.1.51
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RRMA OR B1822
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	RRNA (GUANINE-N(1)-)-METHYLTRANSFERASE, 23S RRNA N1-G745 METHYLTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 23)

No.	Name	Count	Type	Full Name
1	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
2	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE
3	SO4	5	Ligand/Ion	SULFATE ION
4	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:5 , CYS A:8 , CYS A:21 , HIS A:25	BINDING SITE FOR RESIDUE ZN A 1301
2	AC2	SOFTWARE	CYS B:5 , CYS B:8 , CYS B:21 , GLN B:23 , HIS B:25	BINDING SITE FOR RESIDUE ZN B 2301
3	AC3	SOFTWARE	ARG A:71 , HIS A:101 , HOH A:1451	BINDING SITE FOR RESIDUE SO4 A 501
4	AC4	SOFTWARE	ARG B:71 , HIS B:101	BINDING SITE FOR RESIDUE SO4 B 502
5	AC5	SOFTWARE	ARG A:24 , ARG A:182 , SER B:213 , ASN B:261 , HIS B:263	BINDING SITE FOR RESIDUE SO4 B 503
6	AC6	SOFTWARE	ARG B:59 , ARG B:128	BINDING SITE FOR RESIDUE SO4 B 504
7	AC7	SOFTWARE	ARG B:221 , HOH B:2414 , HOH B:2423 , HOH B:2424	BINDING SITE FOR RESIDUE SO4 B 505
8	AC8	SOFTWARE	LEU A:62 , TYR A:67 , GLY A:93 , CYS A:94 , GLY A:95 , GLU A:96 , GLY A:97 , TYR A:98 , TYR A:99 , ILE A:155 , TYR A:156 , THR A:178 , PRO A:179 , HIS A:183 , LEU A:184 , PHE A:260 , HOH A:1434	BINDING SITE FOR RESIDUE SAM A 1401
9	AC9	SOFTWARE	ARG B:58 , TYR B:67 , LEU B:70 , CYS B:94 , GLY B:95 , GLU B:96 , GLY B:97 , TYR B:98 , TYR B:99 , TYR B:156 , HIS B:183 , LEU B:184 , MSE B:233 , THR B:234	BINDING SITE FOR RESIDUE SAM B 2401

Asymmetric/Biological Unit

No.	Residues
1	B:5	-	B:21
2	B:8	-	B:21

(no "Cis Peptide Bond" information available for 1P91)

(no "SAP(SNP)/Variant" information available for 1P91)

(no "PROSITE Motif" information available for 1P91)

(no "Exon" information available for 1P91)

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:268
 aligned with RLMA_ECOLI | P36999 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261        
           RLMA_ECOLI     2 SFSCPLCHQPLSREKNSYICPQRHQFDMAKEGYVNLLPVQHKRSRDPGDSAEMMQARRAFLDAGHYQPLRDAIVAQLRERLDDKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHRLPFSDTSMDAIIRIYAPCKAEELARVVKPGGWVITATPGPRHLMELKGLIYNEVHLHAPHAEQLEGFTLQQSAELCYPMRLRGDEAVALLQMTPFAWRAKPEVWQTLAAKEVFDCQTDFNIHLWQRSY 269
               SCOP domains d1p91a_ A: rRNA methyltransferase RlmA                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eee.....eee......ee..............hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeee......hhhhhhhh....eeeeee.hhhhhhhhhhhh...eeee............eeeeeee....hhhhhhhheeeeeeeeeeee....hhhhhh..................eeeeeeeeeeeeeeeehhhhhhhhhh..hhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p91 A   2 SFSCPLCHQPLSREKNSYICPQRHQFDmAKEGYVNLLPVQHKRSRDPGDSAEmmQARRAFLDAGHYQPLRDAIVAQLRERLDDKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHRLPFSDTSmDAIIRIYAPCKAEELARVVKPGGWVITATPGPRHLmELKGLIYNEVHLHAPHAEQLEGFTLQQSAELCYPmRLRGDEAVALLQmTPFAWRAKPEVWQTLAAKEVFDCQTDFNIHLWQRSY 269
                                    11        21       |31        41        51  ||    61        71        81        91       101       111       121       131       141       151       161       171       181   |   191       201       211       221       231 |     241       251       261        
                                                      29-MSE                   54-MSE                                                                                        149-MSE                             185-MSE                            220-MSE      233-MSE                                
                                                                                55-MSE

Chain B from PDB  Type:PROTEIN  Length:258
 aligned with RLMA_ECOLI | P36999 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261        
           RLMA_ECOLI     2 SFSCPLCHQPLSREKNSYICPQRHQFDMAKEGYVNLLPVQHKRSRDPGDSAEMMQARRAFLDAGHYQPLRDAIVAQLRERLDDKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHRLPFSDTSMDAIIRIYAPCKAEELARVVKPGGWVITATPGPRHLMELKGLIYNEVHLHAPHAEQLEGFTLQQSAELCYPMRLRGDEAVALLQMTPFAWRAKPEVWQTLAAKEVFDCQTDFNIHLWQRSY 269
               SCOP domains d1p91b_ B: rRNA methyltransferase RlmA                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------Methyltransf_31-1p91B01 B:83-246                                                                                                                                    ----------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------Methyltransf_31-1p91B02 B:83-246                                                                                                                                    ----------------------- Pfam domains (2)
         Sec.struct. author ...........ee...eee......ee......ee...----------.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....eeee.......hhhhhhhhh...eeeeee.hhhhhhhhhhhh...eeee............eeeeeee....hhhhhhhheeeeeeeeeeee....hhhhhhhh................eeeeeeeeeeeeeeehhhhhhhhhh...hhhhhhhhhhhhhhhh..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p91 B   2 SFSCPLCHQPLSREKNSYICPQRHQFDmAKEGYVNLLP----------DSAEmmQARRAFLDAGHYQPLRDAIVAQLRERLDDKATAVLDIGCGEGYYTHAFADALPEITTFGLDVSKVAIKAAAKRYPQVTFCVASSHRLPFSDTSmDAIIRIYAPCKAEELARVVKPGGWVITATPGPRHLmELKGLIYNEVHLHAPHAEQLEGFTLQQSAELCYPmRLRGDEAVALLQmTPFAWRAKPEVWQTLAAKEVFDCQTDFNIHLWQRSY 269
                                    11        21       |31       | -        51  ||    61        71        81        91       101       111       121       131       141       151       161       171       181   |   191       201       211       221       231 |     241       251       261        
                                                      29-MSE    39         50   ||                                                                                           149-MSE                             185-MSE                            220-MSE      233-MSE                                
                                                                               54-MSE                                                                                                                                                                                                                   
                                                                                55-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: rRNA methyltransferase RlmA (1)

Protein domain: rRNA methyltransferase RlmA (1)

Escherichia coli [TaxId: 562] (1)

1a	d1p91a_	A:
1b	d1p91b_	B:

(no "CATH Domain" information available for 1P91)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Methyltransf_31 (8)

Escherichia coli (strain K12) (1)

1a	Methyltransf_31-1p91B01	B:83-246
1b	Methyltransf_31-1p91B02	B:83-246

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RLMA_ECOLI | P36999)

molecular function
	GO:0052911	23S rRNA (guanine(745)-N(1))-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + guanine(745) in 23S rRNA = N(1)-methylguanine(745) in 23S rRNA + S-adenosyl-L-homocysteine.
	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:0008989	rRNA (guanine-N1-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N1-methylguanine.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	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:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1p91
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 23)

Sites (9, 9)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (10, 10)

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