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(-) Description

Title :  CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE SIBL IN COMPLEX WITH SAH
 
Authors :  J. S. Liu, S. C. Chen, C. S. Yang, C. H. Huang, Y. Chen
Date :  01 Dec 14  (Deposition) - 25 Nov 15  (Release) - 25 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Sibiromycin Biosynthesis, Sam-Dependent Methyltransferase, C- Methylation. , Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Liu, S. C. Chen, C. S. Yang, C. H. Huang, Y. Chen
Crystal Structure Of S-Adenosylmethionine-Dependent Methyltransferase Sibl In Complex With Sah
To Be Published 2015
PubMed: search

(-) Compounds

Molecule 1 - SIBL
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SIBL
    Organism Scientific: STREPTOSPORANGIUM SIBIRICUM
    Organism Taxid: 457432

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:134 , TYR A:148 , MSE A:151 , SER A:155 , GLY A:178 , GLY A:179 , GLY A:180 , VAL A:183 , ASN A:184 , ASP A:201 , ARG A:202 , ALA A:227 , ASP A:228 , ILE A:229 , ALA A:244 , HIS A:245 , GLN A:246 , ILE A:249 , TRP A:250binding site for residue SAH A 401
2AC2SOFTWARETYR B:134 , TYR B:148 , MSE B:151 , SER B:155 , GLY B:178 , GLY B:179 , GLY B:180 , VAL B:183 , ASN B:184 , ASP B:201 , ARG B:202 , ALA B:227 , ASP B:228 , ILE B:229 , ALA B:244 , HIS B:245 , GLN B:246 , ILE B:249 , TRP B:250binding site for residue SAH B 401
3AC3SOFTWARETYR C:134 , TYR C:148 , MSE C:151 , SER C:155 , GLY C:178 , GLY C:180 , ASN C:184 , ASP C:201 , ARG C:202 , ALA C:227 , ASP C:228 , ILE C:229 , ALA C:244 , HIS C:245 , GLN C:246 , ILE C:249 , TRP C:250binding site for residue SAH C 401
4AC4SOFTWARETYR D:134 , TYR D:148 , MSE D:151 , SER D:155 , GLY D:178 , GLY D:179 , GLY D:180 , VAL D:183 , ASN D:184 , ASP D:201 , ARG D:202 , ALA D:227 , ASP D:228 , ILE D:229 , ALA D:244 , HIS D:245 , GLN D:246 , ILE D:249 , TRP D:250binding site for residue SAH D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X3Q)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Gly A:37 -Pro A:38
2Gly A:285 -Pro A:286
3Gly B:37 -Pro B:38
4Gly B:285 -Pro B:286
5Thr B:333 -Pro B:334
6Gly C:37 -Pro C:38
7Gly C:285 -Pro C:286
8Gly D:37 -Pro D:38
9Gly D:285 -Pro D:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X3Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X3Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4X3Q)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh......eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhh.eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x3q A   4 ELSALVPVLFGHAAFQQLNAGCQLGLFELLHERGPLSAEEVADALRLPRRSADILLLGTTALGLSTVTDGGYRNGAPIGAAFRDGLWPVLRDIVQYQDKIAYQPAADYVESLRTGQNAGIRHFPGTTRDLYSRLAAVPGLEELFYRGmHAWSQLSNPVLLAQPDFTRVHRVLDVGGGDAVNAVALARAHPSLRVTVLDRPGALEVARKTIAEAGLEERVRTHAADIFTDSYPAGHDCVLFAHQLVIWSPEQNLTLLRKAYDAVEPGGRVLVFNAFTDDDRTGPLYAALDNVYFTTLPFRHSTIHRWADCESWLREAGFTDVGRTAPPGWTPHGVVSGSRPR 344
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
                                                                                                                                                                             151-MSE                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eeee..eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhh.eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x3q B   4 ELSALVPVLFGHAAFQQLNAGCQLGLFELLHERGPLSAEEVADALRLPRRSADILLLGTTALGLSTVTDGGYRNGAPIGAAFRDGLWPVLRDIVQYQDKIAYQPAADYVESLRTGQNAGIRHFPGTTRDLYSRLAAVPGLEELFYRGmHAWSQLSNPVLLAQPDFTRVHRVLDVGGGDAVNAVALARAHPSLRVTVLDRPGALEVARKTIAEAGLEERVRTHAADIFTDSYPAGHDCVLFAHQLVIWSPEQNLTLLRKAYDAVEPGGRVLVFNAFTDDDRTGPLYAALDNVYFTTLPFRHSTIHRWADCESWLREAGFTDVGRTAPPGWTPHGVVSGSRPR 344
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
                                                                                                                                                                             151-MSE                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee...........eeeeeee......hhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhh.eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x3q C   4 ELSALVPVLFGHAAFQQLNAGCQLGLFELLHERGPLSAEEVADALRLPRRSADILLLGTTALGLSTVTDGGYRNGAPIGAAFRDGLWPVLRDIVQYQDKIAYQPAADYVESLRTGQNAGIRHFPGTTRDLYSRLAAVPGLEELFYRGmHAWSQLSNPVLLAQPDFTRVHRVLDVGGGDAVNAVALARAHPSLRVTVLDRPGALEVARKTIAEAGLEERVRTHAADIFTDSYPAGHDCVLFAHQLVIWSPEQNLTLLRKAYDAVEPGGRVLVFNAFTDDDRTGPLYAALDNVYFTTLPFRHSTIHRWADCESWLREAGFTDVGRTAPPGWTPHGVVSGSRPR 344
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
                                                                                                                                                                             151-MSE                                                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh......eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x3q D   4 ELSALVPVLFGHAAFQQLNAGCQLGLFELLHERGPLSAEEVADALRLPRRSADILLLGTTALGLSTVTDGGYRNGAPIGAAFRDGLWPVLRDIVQYQDKIAYQPAADYVESLRTGQNAGIRHFPGTTRDLYSRLAAVPGLEELFYRGmHAWSQLSNPVLLAQPDFTRVHRVLDVGGGDAVNAVALARAHPSLRVTVLDRPGALEVARKTIAEAGLEERVRTHAADIFTDSYPAGHDCVLFAHQLVIWSPEQNLTLLRKAYDAVEPGGRVLVFNAFTDDDRTGPLYAALDNVYFTTLPFRHSTIHRWADCESWLREAGFTDVGRTAPPGWTPHGVVSGSRPR 344
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 
                                                                                                                                                                             151-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4X3Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X3Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X3Q)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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        C0LTM6_9ACTN | C0LTM6: 4qvg 4u1q

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