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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF C118A RLMN WITH CROSS-LINKED TRNA PURIFIED FROM ESCHERICHIA COLI
 
Authors :  E. L. Schwalm, T. L. Grove, S. J. Booker, A. K. Boal
Date :  22 Jan 16  (Deposition) - 13 Apr 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Rna Complex, Radical Sam Enzyme, Transfer Rna, Iron-Sulfur Cluster, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. L. Schwalm, T. L. Grove, S. J. Booker, A. K. Boal
Crystallographic Capture Of A Radical S-Adenosylmethionine Enzyme In The Act Of Modifying Trna.
Science V. 352 309 2016
PubMed-ID: 27081063  |  Reference-DOI: 10.1126/SCIENCE.AAD5367

(-) Compounds

Molecule 1 - RLMN METHYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 23S RRNA (ADENINE(2503)-C(2))-METHYLTRANSFERASE,23S RRNA M2A2503 METHYLTRANSFERASE,RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE N,TRNA (ADENINE(37)-C(2))-METHYLTRANSFERASE,TRNA M2A37 METHYLTRANSFERASE
 
Molecule 2 - TRNA GLU
    Chains: C, D
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 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  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
15AD2Ligand/Ion5'-DEOXYADENOSINE
2MET2Mod. Amino AcidMETHIONINE
3MG6Ligand/IonMAGNESIUM ION
4SF42Ligand/IonIRON/SULFUR CLUSTER
5SMC2Mod. Amino AcidS-METHYLCYSTEINE
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
15AD1Ligand/Ion5'-DEOXYADENOSINE
2MET1Mod. Amino AcidMETHIONINE
3MG-1Ligand/IonMAGNESIUM ION
4SF41Ligand/IonIRON/SULFUR CLUSTER
5SMC1Mod. Amino AcidS-METHYLCYSTEINE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
15AD1Ligand/Ion5'-DEOXYADENOSINE
2MET1Mod. Amino AcidMETHIONINE
3MG-1Ligand/IonMAGNESIUM ION
4SF41Ligand/IonIRON/SULFUR CLUSTER
5SMC1Mod. Amino AcidS-METHYLCYSTEINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:175 , GLY A:177 , GLY A:179 , GLU A:180 , SER A:211 , THR A:212 , SER A:213 , SER A:233 , SF4 A:502 , 5AD A:503binding site for residue MET A 501
02AC2SOFTWARECYS A:125 , CYS A:129 , CYS A:132 , SER A:213 , MET A:501binding site for residue SF4 A 502
03AC3SOFTWAREPHE A:131 , CYS A:132 , SER A:233 , HIS A:235 , GLU A:278 , VAL A:280 , ILE A:309 , TRP A:311 , ASN A:312 , SMC A:355 , GLY A:356 , MET A:501binding site for residue 5AD A 503
04AC4SOFTWARELEU A:196 , LEU A:203 , A C:26binding site for residue MG A 504
05AC5SOFTWAREHOH A:610 , C C:38 , G C:39 , HOH C:202binding site for residue MG C 101
06AC6SOFTWAREU C:7 , C C:8binding site for residue MG C 102
07AC7SOFTWAREU C:7 , A C:13 , G C:14binding site for residue MG C 103
08AC8SOFTWAREGLY B:177 , GLY B:179 , GLU B:180 , SER B:211 , THR B:212 , SER B:213 , SER B:233 , SF4 B:502 , 5AD B:503binding site for residue MET B 501
09AC9SOFTWARECYS B:125 , LEU B:127 , CYS B:129 , CYS B:132 , ALA B:135 , SER B:213 , MET B:501binding site for residue SF4 B 502
10AD1SOFTWAREPHE B:131 , CYS B:132 , SER B:233 , HIS B:235 , GLU B:278 , VAL B:280 , ILE B:309 , TRP B:311 , ASN B:312 , SMC B:355 , GLY B:356 , MET B:501 , HOH B:603binding site for residue 5AD B 503
11AD2SOFTWARELEU B:196 , ASP B:198 , LEU B:203 , HOH B:607 , A D:26 , HOH D:201binding site for residue MG B 504
12AD3SOFTWAREHOH B:614 , C D:38 , G D:39 , HOH D:203binding site for residue MG D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HR6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:360 -Asp B:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HR6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HR6)

(-) Exons   (0, 0)

(no "Exon" information available for 5HR6)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhh......eeeeee.....eeeeeee..eeeeeeeeee..eeeee...eee.......hhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhh......hhh.eeeee..hhhhhhhhhh....eeeee....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......eeeeeee......hhhhhhhhhhhh....eeeeeee............hhhhhhhhhhhhhhh...eee....hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hr6 A  18 INLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDEMTDINKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRATLAVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAAcGQLAGDVIDRTKRTLRM 501
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367   ||
                                                                                                                                                                                                                                                                                                                                                                           355-SMC         371|
                                                                                                                                                                                                                                                                                                                                                                                            501


Chain B from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhh.....hhhhhhhhhh......eeeeee.....eeeeeee..eeeeeeeeee..eeeee...eee.......hhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhhhh......hhh.eeeee..hhhhhhhhhh....eeeee....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......eeeeeee......hhhhhhhhhhhh....eeeeeee............hhhhhhhhhhhhhhh...eee....hhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hr6 B  18 INLLDLNRQQMREFFKDLGEKPFRADQVMKWMYHYCCDNFDEMTDINKVLRGKLKEVAEIRAPEVVEEQRSSDGTIKWAIAVGDQRVETVYIPEDDRATLAVSSQVGCALECKFCSTAQQGFNRNLRVSEIIGQVWRAAKIVGAAKVTGQRPITNVVMMGMGEPLLNLNNVVPAMEIMLDDFGFGLSKRRVTLSTSGVVPALDKLGDMIDVALAISLHAPNDEIRDEIVPINKKYNIETFLAAVRRYLEKSNANQGRVTIEYVMLDHVNDGTEHAHQLAELLKDTPCKINLIPWNPFPGAPYGRSSNSRIDRFSKVLMSYGFTTIVRKTRGDDIDAAcGQLAGDVIDRTKRTLRM 501
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367   ||
                                                                                                                                                                                                                                                                                                                                                                           355-SMC         371|
                                                                                                                                                                                                                                                                                                                                                                                            501


Chain C from PDB  Type:RNA  Length:68
                                                                                                    
                 5hr6 C   2 CCCCUUCGUCUAGAGGCCCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGGG  69
                                    11        21        31        41        51        61        


Chain D from PDB  Type:RNA  Length:66
                                                                                                  
                 5hr6 D   3 CCCUUCGUCUAGAGGCCCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGG  68
                                    12        22        32        42        52        62
   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  (0, 0)

(no "SCOP Domain" information available for 5HR6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HR6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HR6)

(-) Gene Ontology  (20, 37)

Asymmetric Unit(hide GO term definitions)

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  RLMN_ECO24 | A7ZPW0
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  RLMN_ECOLI | P36979
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 Related Entries

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

UniProtKB/Swiss-Prot
        RLMN_ECO24 | A7ZPW0: 5hr7
        RLMN_ECOLI | P36979: 3rf9 3rfa 5hr7

(-) Related Entries Specified in the PDB File

5hr7