4ATN - JenaLib

Title :   CRYSTAL STRUCTURE OF C2498 2'-O-RIBOSE METHYLTRANSFERASE RLMM FROM ESCHERICHIA COLI

Authors :   A. S. Punekar, T. R. Shepherd, J. Liljeruhm, A. C. Forster, M. Selmer

Date :   08 May 12 (Deposition) - 15 Aug 12 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Punekar, T. R. Shepherd, J. Liljeruhm, A. C. Forster, M. Selmer
Crystal Structure Of Rlmm, The 2'O-Ribose Methyltransferase For C2498 Of Escherichia Coli 23S Rrna.
Nucleic Acids Res. V. 40 10507 2012
PubMed-ID: 22923526 | Reference-DOI: 10.1093/NAR/GKS727

Compounds

Molecule 1 - RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
	Chains	:	A
	EC Number	:	2.1.1.186
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEXP5-CT/TOPO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Strain	:	K-12
	Synonym	:	23S RRNA (CYTIDINE2498-2'-O)-METHYLTRANSFERASE, 23S RRNA 2'-O-RIBOSE METHYLTRANSFERASE RLMM

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 31)

Asymmetric/Biological Unit (4, 31)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	EDO	21	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	5	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Sites (30, 30)

Asymmetric Unit (30, 30)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:34 , LYS A:36 , TYR A:41 , VAL A:42 , ILE A:43 , HOH A:2035	BINDING SITE FOR RESIDUE GOL A1358
02	AC2	SOFTWARE	ARG A:85 , ASN A:211 , ASN A:233 , GLN A:253 , HOH A:2147 , HOH A:2189	BINDING SITE FOR RESIDUE GOL A1359
03	AC3	SOFTWARE	VAL A:96 , VAL A:97 , GLU A:98 , ARG A:145 , PRO A:146 , TYR A:164	BINDING SITE FOR RESIDUE GOL A1360
04	AC4	SOFTWARE	SER A:62 , SER A:63 , ILE A:65 , LEU A:320 , GLN A:337 , ALA A:338 , EDO A:1375 , HOH A:2026 , HOH A:2190 , HOH A:2191	BINDING SITE FOR RESIDUE GOL A1361
05	AC5	SOFTWARE	PHE A:171 , PRO A:176 , ARG A:177 , HOH A:2110	BINDING SITE FOR RESIDUE GOL A1362
06	AC6	SOFTWARE	PHE A:264 , THR A:267 , ARG A:268	BINDING SITE FOR RESIDUE EDO A1363
07	AC7	SOFTWARE	PHE A:61 , SER A:62 , ASN A:167 , EDO A:1373	BINDING SITE FOR RESIDUE EDO A1364
08	AC8	SOFTWARE	THR A:110 , ASN A:111 , GLU A:112 , PRO A:222 , PRO A:243 , HOH A:2041 , HOH A:2088 , HOH A:2150	BINDING SITE FOR RESIDUE EDO A1365
09	AC9	SOFTWARE	ASP A:109 , LYS A:114 , HOH A:2085 , HOH A:2192	BINDING SITE FOR RESIDUE EDO A1366
10	BC1	SOFTWARE	THR A:21 , PHE A:32 , ALA A:33 , HOH A:2017 , HOH A:2193	BINDING SITE FOR RESIDUE EDO A1367
11	BC2	SOFTWARE	LYS A:281 , PRO A:308 , MET A:309 , LYS A:310	BINDING SITE FOR RESIDUE EDO A1368
12	BC3	SOFTWARE	ALA A:18 , TYR A:313 , GLU A:314 , HOH A:2018	BINDING SITE FOR RESIDUE EDO A1369
13	BC4	SOFTWARE	ARG A:34 , VAL A:35 , EDO A:1371	BINDING SITE FOR RESIDUE EDO A1370
14	BC5	SOFTWARE	ARG A:34 , GLU A:259 , ASP A:260 , EDO A:1370	BINDING SITE FOR RESIDUE EDO A1371
15	BC6	SOFTWARE	GLN A:48 , PRO A:49 , ASP A:50 , ASP A:51 , HIS A:330 , HOH A:2046 , HOH A:2047	BINDING SITE FOR RESIDUE EDO A1372
16	BC7	SOFTWARE	ARG A:57 , ASN A:167 , EDO A:1364 , EDO A:1376	BINDING SITE FOR RESIDUE EDO A1373
17	BC8	SOFTWARE	ASP A:22 , HOH A:2171	BINDING SITE FOR RESIDUE EDO A1374
18	BC9	SOFTWARE	SER A:62 , SER A:63 , ILE A:336 , GOL A:1361 , HOH A:2194 , HOH A:2195	BINDING SITE FOR RESIDUE EDO A1375
19	CC1	SOFTWARE	ARG A:57 , ASN A:166 , ASN A:167 , EDO A:1373	BINDING SITE FOR RESIDUE EDO A1376
20	CC2	SOFTWARE	GLY A:91 , MET A:92 , HOH A:2065	BINDING SITE FOR RESIDUE EDO A1377
21	CC3	SOFTWARE	LYS A:99 , ARG A:132 , ASP A:133 , GLY A:135 , TYR A:140	BINDING SITE FOR RESIDUE EDO A1378
22	CC4	SOFTWARE	PRO A:82 , ARG A:85 , VAL A:230 , ASN A:233 , GLN A:253	BINDING SITE FOR RESIDUE EDO A1379
23	CC5	SOFTWARE	SER A:269 , ILE A:271 , GLY A:296 , TRP A:356	BINDING SITE FOR RESIDUE EDO A1380
24	CC6	SOFTWARE	ILE A:332 , ASN A:333 , ARG A:354 , ILE A:355	BINDING SITE FOR RESIDUE EDO A1381
25	CC7	SOFTWARE	ARG A:187 , HIS A:343 , SO4 A:1387 , HOH A:2122	BINDING SITE FOR RESIDUE EDO A1382
26	CC8	SOFTWARE	ASP A:206	BINDING SITE FOR RESIDUE EDO A1383
27	CC9	SOFTWARE	LYS A:99 , ALA A:138 , ASN A:139 , TYR A:140	BINDING SITE FOR RESIDUE SO4 A1384
28	DC1	SOFTWARE	LYS A:118 , ARG A:121 , LYS A:122 , SO4 A:1386	BINDING SITE FOR RESIDUE SO4 A1385
29	DC2	SOFTWARE	ARG A:121 , LYS A:122 , TRP A:214 , ARG A:268 , ASN A:270 , SO4 A:1385	BINDING SITE FOR RESIDUE SO4 A1386
30	DC3	SOFTWARE	ARG A:187 , SER A:188 , LYS A:191 , ARG A:345 , EDO A:1382 , HOH A:2122	BINDING SITE FOR RESIDUE SO4 A1387

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:357
 aligned with RLMM_ECOLI | P0ADR6 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:357
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       
           RLMM_ECOLI     1 MNKVVLLCRPGFEKECAAEITDKAGQREIFGFARVKENAGYVIYECYQPDDGDKLIRELPFSSLIFARQWFVVGELLQHLPPEDRITPIVGMLQGVVEKGGELRVEVADTNESKELLKFCRKFTVPLRAALRDAGVLANYETPKRPVVHVFFIAPGCCYTGYSYSNNNSPFYMGIPRLKFPADAPSRSTLKLEEAFHVFIPADEWDERLANGMWAVDLGACPGGWTYQLVKRNMWVYSVDNGPMAQSLMDTGQVTWLREDGFKFRPTRSNISWMVCDMVEKPAKVAALMAQWLVNGWCRETIFNLKLPMKKRYEEVSHNLAYIQAQLDEHGINAQIQARQLYHDREEVTVHVRRIWA 357
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhhhhhhhh....eee.......eeeeee...hhhhhhhhhh.hhh.....eeeee............hhhhhhhhh.......eeeeee.....hhhhhhhhhhhhhhhhhhhhhh............eeeeeeee..eeeeeee........hhh.............hhhhhhhhhhhhh.hhhhhhh.....eeeee....hhhhhhhhhh..eeeee.....hhhhhh...eeee.............eeeeee....hhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4atn A   1 MNKVVLLCRPGFEKECAAEITDKAGQREIFGFARVKENAGYVIYECYQPDDGDKLIRELPFSSLIFARQWFVVGELLQHLPPEDRITPIVGMLQGVVEKGGELRVEVADTNESKELLKFCRKFTVPLRAALRDAGVLANYETPKRPVVHVFFIAPGcCYTGYSYSNNNSPFYMGIPRLKFPADAPSRSTLKLEEAFHVFIPADEWDERLANGMWAVDLGACPGGWTYQLVKRNMWVYSVDNGPMAQSLMDTGQVTWLREDGFKFRPTRSNISWMVCDMVEKPAKVAALMAQWLVNGWCRETIFNLKLPMKKRYEEVSHNLAYIQAQLDEHGINAQIQARQLYHDREEVTVHVRRIWA 357
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      |160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       
                                                                                                                                                                                      157-CSS

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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