5JR3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CARMINOMYCIN-4-O-METHYLTRANSFERASE DNRK IN COMPLEX WITH SAH AND 4-METHYLUMBELLIFERONE

Authors :   F. Wang, B. R. Johnson, T. D. Huber, S. Singh, J. S. Thorson, G. N. Phillip Enzyme Discovery For Natural Product Biosynthesis (Natpro)

Date :   05 May 16 (Deposition) - 01 Jun 16 (Release) - 01 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (2x)
Biol. Unit 2: B,C  (1x)

Keywords :   Natural Product Biosynthesis, Structural Genomics, Psi-Biology, Protein Structure Initiative, Enzyme Discovery For Natural Product Biosynthesis, Natpro, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Wang, B. R. Johnson, T. D. Huber, S. Singh, J. S. Thorson, G. N. Phillips Jr.
Crystal Structure Of Carminomycin-4-O-Methyltransferase Dnr In Complex With Sah And 4-Methylumbelliferone (To Be Published)
To Be Published
PubMed: search

Molecule 1 - CARMINOMYCIN 4-O-METHYLTRANSFERASE DNRK
	Chains	:	A, B, C
	EC Number	:	2.1.1.292
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RESIDUES 10-353
	Gene	:	DNRK
	Organism Scientific	:	STREPTOMYCES PEUCETIUS
	Organism Taxid	:	1950
	Synonym	:	COMT,ANTHRACYCLINE 4-O-METHYLTRANSFERASE

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	4MU	3	Ligand/Ion	7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE
2	SAH	3	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	4MU	2	Ligand/Ion	7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	4MU	2	Ligand/Ion	7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE
2	SAH	2	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
3	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:143 , ARG A:153 , LEU A:160 , GLY A:187 , GLU A:210 , MET A:211 , GLY A:236 , ASP A:237 , PHE A:238 , SER A:252 , PHE A:253 , ASN A:257 , HOH A:550 , HOH A:569 , HOH A:604 , HOH A:611 , HOH A:614 , HOH A:670 , HOH A:693	binding site for residue SAH A 401
02	AC2	SOFTWARE	PHE A:156 , PHE A:253 , LEU A:300 , ARG A:303 , HOH A:584	binding site for residue 4MU A 402
03	AC3	SOFTWARE	ARG A:115 , ARG A:149 , HOH A:559 , HOH A:580 , HOH A:623 , HIS B:261	binding site for residue SO4 A 403
04	AC4	SOFTWARE	ARG A:57 , HOH A:502 , HOH A:503	binding site for residue SO4 A 404
05	AC5	SOFTWARE	ARG A:219 , ASP A:232 , VAL A:233 , HOH A:541	binding site for residue SO4 A 405
06	AC6	SOFTWARE	LYS A:52 , HOH A:711 , THR C:50 , LYS C:52 , ALA C:53	binding site for residue SO4 A 406
07	AC7	SOFTWARE	TYR B:143 , ARG B:153 , LEU B:160 , GLY B:187 , GLU B:210 , MET B:211 , GLY B:236 , ASP B:237 , PHE B:238 , SER B:252 , PHE B:253 , ASN B:257 , HOH B:522 , HOH B:559 , HOH B:605 , HOH B:619 , HOH B:629 , HOH B:633 , HOH B:683	binding site for residue SAH B 401
08	AC8	SOFTWARE	PHE B:156 , LEU B:300 , ARG B:303 , HOH B:606	binding site for residue 4MU B 402
09	AC9	SOFTWARE	ARG A:61 , ARG A:131 , PRO A:259 , HIS A:261 , HOH A:643 , HOH B:502 , HOH B:519	binding site for residue SO4 B 403
10	AD1	SOFTWARE	ARG B:115 , ARG B:149 , HOH B:521	binding site for residue SO4 B 404
11	AD2	SOFTWARE	ARG B:61 , PRO B:62 , GLU B:63 , HOH B:541	binding site for residue SO4 B 405
12	AD3	SOFTWARE	ARG A:128 , ARG B:131 , PRO B:259 , HIS B:261 , HOH B:543 , HOH B:607 , ARG C:61	binding site for residue SO4 B 406
13	AD4	SOFTWARE	HIS B:289 , THR B:314 , LYS B:317 , HOH B:511 , HOH B:594 , HOH B:693 , GLU C:63 , LEU C:66 , ARG C:70	binding site for residue SO4 B 407
14	AD5	SOFTWARE	ARG B:219 , ASP B:232 , VAL B:233 , HOH B:504 , HOH B:618	binding site for residue SO4 B 408
15	AD6	SOFTWARE	TYR C:143 , ARG C:153 , LEU C:160 , GLY C:187 , GLU C:210 , MET C:211 , GLY C:236 , ASP C:237 , PHE C:238 , SER C:252 , PHE C:253 , ASN C:257 , TRP C:258 , HOH C:522 , HOH C:594 , HOH C:595 , HOH C:643	binding site for residue SAH C 401
16	AD7	SOFTWARE	PHE C:156 , LEU C:160 , LEU C:300 , ARG C:303 , MET C:304 , HOH C:627	binding site for residue 4MU C 402
17	AD8	SOFTWARE	ARG C:115 , ARG C:149 , HOH C:617 , HOH C:632	binding site for residue SO4 C 403
18	AD9	SOFTWARE	HIS C:43 , ALA C:46 , ARG C:57 , HOH C:517 , HOH C:658	binding site for residue SO4 C 404

(no "SS Bond" information available for 5JR3)

(no "Cis Peptide Bond" information available for 5JR3)

(no "SAP(SNP)/Variant" information available for 5JR3)

(no "PROSITE Motif" information available for 5JR3)

(no "Exon" information available for 5JR3)

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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr3 A  11 PQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPAA 353
                                    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

Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr3 B  13 QIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPA 352
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain C from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......eeeee....hhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jr3 C  10 RPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTELDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPAA 353
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349

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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 '\|'

(no "SCOP Domain" information available for 5JR3)

(no "CATH Domain" information available for 5JR3)

(no "Pfam Domain" information available for 5JR3)

Asymmetric Unit(hide GO term definitions)

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5jr3)

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(no "Related Entries Specified in the PDB File" available for 5JR3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (6, 6)

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