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(-) Description

Title :  CRYSTAL STRUCTURE OF S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE SIBL IN COMPLEX WITH 3HK AND SAH
 
Authors :  J. S. Liu, S. C. Chen, C. S. Yang, C. H. Huang, Y. Chen
Date :  16 Jul 14  (Deposition) - 05 Aug 15  (Release) - 05 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Methyltransferase, Transferase (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 3Hk And Sah
To Be Published
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
13DJ4Ligand/Ion(2S)-2-AMINO-4-(2-AMINO-3-HYDROXYPHENYL)-4-OXOBUTANOICACID
2SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
13DJ2Ligand/Ion(2S)-2-AMINO-4-(2-AMINO-3-HYDROXYPHENYL)-4-OXOBUTANOICACID
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
13DJ2Ligand/Ion(2S)-2-AMINO-4-(2-AMINO-3-HYDROXYPHENYL)-4-OXOBUTANOICACID
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:99 , TYR A:134 , PHE A:147 , MET A:151 , TRP A:154 , HIS A:245 , ALA A:277 , TYR A:288 , ASP A:292 , TYR A:295 , PHE A:296 , HIS A:335 , HOH A:531 , HOH A:552binding site for residue 3DJ A 400
2AC2SOFTWARETYR A:148 , MET 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:250 , HOH A:548 , HOH A:558 , HOH A:695binding site for residue SAH A 401
3AC3SOFTWARETYR B:99 , TYR B:134 , PHE B:147 , MET B:151 , TRP B:154 , HIS B:245 , ALA B:277 , TYR B:288 , ASP B:292 , TYR B:295 , PHE B:296 , HIS B:335 , HOH B:526 , HOH B:534binding site for residue 3DJ B 400
4AC4SOFTWARETYR B:148 , MET 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:250 , HOH B:535 , HOH B:538binding site for residue SAH B 401
5AC5SOFTWARETYR C:99 , TYR C:134 , PHE C:147 , MET C:151 , TRP C:154 , HIS C:245 , VAL C:248 , ALA C:277 , TYR C:288 , ASP C:292 , TYR C:295 , PHE C:296 , HIS C:335 , HOH C:523 , HOH C:539binding site for residue 3DJ C 400
6AC6SOFTWARETYR C:148 , MET C:151 , SER C:155 , GLY C:178 , GLY C:179 , GLY C:180 , VAL C:183 , 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:250 , HOH C:521 , HOH C:534 , HOH C:574binding site for residue SAH C 401
7AC7SOFTWARETYR D:99 , TYR D:134 , PHE D:147 , MET D:151 , TRP D:154 , HIS D:245 , ALA D:277 , TYR D:288 , ASP D:292 , TYR D:295 , PHE D:296 , HIS D:335 , HOH D:524 , HOH D:556binding site for residue 3DJ D 400
8AC8SOFTWARETYR D:148 , MET 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:250 , HOH D:522 , HOH D:533 , HOH D:535binding site for residue SAH D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U1Q)

(-) Cis Peptide Bonds  (8, 8)

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
5Gly C:37 -Pro C:38
6Gly C:285 -Pro C:286
7Gly D:37 -Pro D:38
8Gly D:285 -Pro D:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U1Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U1Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4U1Q)

(-) 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..hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u1q 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 


Chain B 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...eeeeeehhhhhhhhhhhhhhhh....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u1q 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 


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.hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u1q 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 


Chain D 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.hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh....eeeee...........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........hhhhhhhhhhhhhh........hhhhhhhhhhhhh.eeeeee.......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u1q 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
   Legend:   → Mismatch (orange background)
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  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 4U1Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U1Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U1Q)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        C0LTM6_9ACTN | C0LTM6: 4qvg 4x3q

(-) Related Entries Specified in the PDB File

4qvg APO-FORM STRUCTURE