3PX3 - JenaLib

Title :   STRUCTURE OF TYLM1 FROM STREPTOMYCES FRADIAE H123A MUTANT IN COMPLEX WITH SAH AND DTDP-QUIP3N

Authors :   H. M. Holden, A. E. Carney

Date :   09 Dec 10 (Deposition) - 22 Dec 10 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Sam Binding, N, N-Dimethyltransferase, Dtdp-Quip3N Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. E. Carney, H. M. Holden
Molecular Architecture Of Tylm1 From Streptomyces Fradiae: An N, N-Dimethyltransferase Involved In The Production Of Dtdp-D-Mycaminose .
Biochemistry V. 50 780 2011
PubMed-ID: 21142177 | Reference-DOI: 10.1021/BI101733Y

Compounds

Molecule 1 - N-METHYLTRANSFERASE
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET31B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TYLM1, TYLMI(ORF3*)
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES FRADIAE
	Organism Taxid	:	1906
	Strain	:	ATCC 19609

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	T3Q	2	Ligand/Ion	[(3R,4S,5S,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:14 , TYR A:22 , TYR A:33 , ALA A:58 , GLY A:60 , HIS A:64 , GLU A:79 , LEU A:80 , SER A:81 , ASP A:101 , MET A:102 , MET A:117 , PHE A:118 , SER A:120 , ALA A:123 , HOH A:268 , HOH A:283 , T3Q A:301 , HOH A:311 , HOH A:350 , HOH A:354 , HOH A:391	BINDING SITE FOR RESIDUE SAH A 264
2	AC2	SOFTWARE	TYR A:14 , HIS A:26 , LYS A:29 , PHE A:118 , TRP A:152 , TRP A:153 , PHE A:158 , THR A:159 , TYR A:162 , ALA A:164 , ARG A:177 , SER A:179 , SER A:181 , ILE A:190 , ARG A:241 , SAH A:264 , HOH A:277 , HOH A:282 , HOH A:289 , HOH A:349 , HOH A:359	BINDING SITE FOR RESIDUE T3Q A 301
3	AC3	SOFTWARE	GLY A:126 , GLU A:186 , THR A:213 , PHE A:215 , GLN A:219 , HOH A:402	BINDING SITE FOR RESIDUE EDO A 265
4	AC4	SOFTWARE	TYR D:14 , TYR D:22 , TYR D:33 , ALA D:58 , GLY D:60 , HIS D:64 , GLU D:79 , LEU D:80 , MET D:84 , ASP D:101 , MET D:102 , MET D:117 , PHE D:118 , SER D:120 , ALA D:123 , HOH D:274 , HOH D:292 , HOH D:293 , T3Q D:301 , HOH D:324 , HOH D:326 , HOH D:401	BINDING SITE FOR RESIDUE SAH D 264
5	AC5	SOFTWARE	TYR D:14 , HIS D:26 , LYS D:29 , PHE D:118 , TRP D:152 , TRP D:153 , PHE D:158 , THR D:159 , TYR D:162 , ALA D:164 , ARG D:177 , SER D:179 , SER D:181 , ILE D:190 , ARG D:241 , SAH D:264 , HOH D:281 , HOH D:296 , HOH D:319 , HOH D:385 , HOH D:408	BINDING SITE FOR RESIDUE T3Q D 301

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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)
	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:240
 aligned with TYLM1_STRFR | P95748 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:240
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
          TYLM1_STRFR    10 PQADYSGEIAELYDLVHQGKGKDYHREAADLAALVRRHSPKAASLLDVACGTGMHLRHLADSFGTVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLGRRFSAVTCMFSSIGHLAGQAELDAALERFAAHVLPDGVVVVEPWWFPENFTPGYVAAGTVEAGGTTVTRVSHSSREGEATRIEVHYLVAGPDRGITHHEESHRITLFTREQYERAFTAAGLSVEFMPGGPSGRGLFTGLPG 249
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhh....eeeeee.hhhhhhhhhhhh...eeee...........eeeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.............eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeee..hhhhhhhhhhhh.eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3px3 A  10 PQADYSGEIAELYDLVHQGKGKDYHREAADLAALVRRHSPKAASLLDVACGTGMHLRHLADSFGTVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLGRRFSAVTCMFSSIGALAGQAELDAALERFAAHVLPDGVVVVEPWWFPENFTPGYVAAGTVEAGGTTVTRVSHSSREGEATRIEVHYLVAGPDRGITHHEESHRITLFTREQYERAFTAAGLSVEFMPGGPSGRGLFTGLPG 249
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

Chain D from PDB  Type:PROTEIN  Length:240
 aligned with TYLM1_STRFR | P95748 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:240
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
          TYLM1_STRFR    10 PQADYSGEIAELYDLVHQGKGKDYHREAADLAALVRRHSPKAASLLDVACGTGMHLRHLADSFGTVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLGRRFSAVTCMFSSIGHLAGQAELDAALERFAAHVLPDGVVVVEPWWFPENFTPGYVAAGTVEAGGTTVTRVSHSSREGEATRIEVHYLVAGPDRGITHHEESHRITLFTREQYERAFTAAGLSVEFMPGGPSGRGLFTGLPG 249
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhh....eeeeee.hhhhhhhhhhhh...eeee...........eeeeee..hhhhhh.hhhhhhhhhhhhhh.eeeeeeeee....hhhhh....eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeee..hhhhhhhhhhhh.eeeeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3px3 D  10 PQADYSGEIAELYDLVHQGKGKDYHREAADLAALVRRHSPKAASLLDVACGTGMHLRHLADSFGTVEGLELSADMLAIARRRNPDAVLHHGDMRDFSLGRRFSAVTCMFSSIGALAGQAELDAALERFAAHVLPDGVVVVEPWWFPENFTPGYVAAGTVEAGGTTVTRVSHSSREGEATRIEVHYLVAGPDRGITHHEESHRITLFTREQYERAFTAAGLSVEFMPGGPSGRGLFTGLPG 249
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

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Gene Ontology (6, 6)

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	3px3
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