2Y3S - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF THE TIRANDAMYCINE-BOUND FAD-DEPENDENT TIRANDAMYCIN OXIDASE TAML IN C2 SPACE GROUP

Authors :   J. C. Carlson, S. Li, S. S. Gunatilleke, Y. Anzai, D. A. Burr, L. M. Podust D. H. Sherman

Date :   23 Dec 10 (Deposition) - 29 Jun 11 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Carlson, S. Li, S. S. Gunatilleke, Y. Anzai, D. A. Burr, L. M. Podust, D. H. Sherman
Tirandamycin Biosynthesis Is Mediated By Co-Dependent Oxidative Enzymes
Nat. Chem V. 3 628 2011
PubMed-ID: 21778983 | Reference-DOI: 10.1038/NCHEM.1087

Molecule 1 - TAML
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	CODON PLUS RP
	Expression System Vector	:	PSJ2
	Organism Scientific	:	STREPTOMYCES SP. 307-9
	Organism Taxid	:	529089
	Other Details	:	COVALENT LINK BETWEEN 8-ALPHA METHYL GROUP OF FAD TO N-1 OF HIS 62. COVALENT LINK BETWEEN C-6 ATOM OF FAD AND CYS 122

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 16)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	GOL	5	Ligand/Ion	GLYCEROL
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	TIR	2	Ligand/Ion	TIRANDAMYCIN E

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:57 , ARG A:58 , SER A:59 , GLY A:60 , GLY A:61 , HIS A:62 , CYS A:63 , TYR A:64 , PHE A:67 , VAL A:68 , ALA A:98 , GLY A:120 , ALA A:121 , CYS A:122 , VAL A:125 , GLY A:126 , GLY A:128 , GLY A:129 , HIS A:130 , LEU A:132 , TYR A:136 , GLY A:189 , GLY A:190 , GLY A:193 , VAL A:195 , MET A:333 , TYR A:444 , ASN A:446 , TIR A:700 , HOH A:2063 , HOH A:2381 , HOH A:2446 , HOH A:2447 , HOH A:2448	BINDING SITE FOR RESIDUE FAD A 600
02	AC2	SOFTWARE	TYR A:64 , CYS A:122 , TYR A:264 , ASP A:332 , THR A:334 , ALA A:337 , ILE A:339 , ALA A:373 , VAL A:403 , TYR A:447 , FAD A:600 , MG A:800 , HOH A:2073 , HOH A:2292 , HOH A:2293 , HOH A:2350 , HOH A:2449 , HOH A:2450 , HOH A:2451 , HOH A:2452	BINDING SITE FOR RESIDUE TIR A 700
03	AC3	SOFTWARE	TIR A:700 , HOH A:2292 , HOH A:2293 , HOH A:2350 , HOH A:2449	BINDING SITE FOR RESIDUE MG A 800
04	AC4	SOFTWARE	VAL B:57 , ARG B:58 , SER B:59 , GLY B:60 , GLY B:61 , HIS B:62 , CYS B:63 , TYR B:64 , PHE B:67 , VAL B:68 , ALA B:98 , GLY B:120 , ALA B:121 , CYS B:122 , VAL B:125 , GLY B:126 , GLY B:128 , GLY B:129 , HIS B:130 , GLY B:135 , TYR B:136 , GLY B:189 , GLY B:190 , GLY B:193 , VAL B:195 , TYR B:444 , ASN B:446 , TIR B:700 , HOH B:2348 , HOH B:2421 , HOH B:2422 , HOH B:2423 , HOH B:2424	BINDING SITE FOR RESIDUE FAD B 600
05	AC5	SOFTWARE	TYR B:64 , CYS B:122 , ASP B:332 , THR B:334 , ALA B:337 , ILE B:339 , ALA B:373 , THR B:405 , TYR B:447 , FAD B:600 , MG B:800 , HOH B:2268 , HOH B:2321 , HOH B:2425 , HOH B:2426 , HOH B:2427 , HOH B:2428 , HOH B:2429 , HOH B:2430	BINDING SITE FOR RESIDUE TIR B 700
06	AC6	SOFTWARE	TIR B:700 , HOH B:2266 , HOH B:2268 , HOH B:2321 , HOH B:2429	BINDING SITE FOR RESIDUE MG B 800
07	AC7	SOFTWARE	LYS A:107 , ARG A:111 , LEU A:319 , HIS A:320 , ARG A:323 , HOH A:2453 , HOH A:2454 , GLU B:21 , HOH B:2017	BINDING SITE FOR RESIDUE GOL A1501
08	AC8	SOFTWARE	PRO B:138 , LEU B:139 , ARG B:141 , MET B:142 , CYS B:261 , ASP B:262 , LEU B:263 , TYR B:264 , GLN B:282	BINDING SITE FOR RESIDUE GOL B1501
09	AC9	SOFTWARE	HIS B:151 , ARG B:171 , GLU B:172	BINDING SITE FOR RESIDUE CL B1502
10	BC1	SOFTWARE	GLU B:31 , HIS B:33 , VAL B:44 , ARG B:47 , ALA B:48 , VAL B:75 , HOH B:2431 , HOH B:2432	BINDING SITE FOR RESIDUE GOL B1503
11	BC2	SOFTWARE	VAL A:85 , GLY A:86 , PHE A:87 , ASP A:88 , HOH A:2455 , HOH A:2456	BINDING SITE FOR RESIDUE GOL A1502
12	BC3	SOFTWARE	PRO A:138 , LEU A:139 , ARG A:141 , MET A:142 , CYS A:261 , ASP A:262 , LEU A:263 , GLN A:282 , ASP A:284	BINDING SITE FOR RESIDUE GOL A1503
13	BC4	SOFTWARE	ALA A:38 , ARG A:197 , HOH A:2151	BINDING SITE FOR RESIDUE CL A1504
14	BC5	SOFTWARE	VAL B:266 , THR B:280	BINDING SITE FOR RESIDUE CL B1504
15	BC6	SOFTWARE	ASP A:66 , ASN A:70 , ALA A:492	BINDING SITE FOR RESIDUE CL A1505
16	BC7	SOFTWARE	ASP B:66 , ASN B:70 , ALA B:492	BINDING SITE FOR RESIDUE CL B1505

(no "SS Bond" information available for 2Y3S)

(no "Cis Peptide Bond" information available for 2Y3S)

(no "SAP(SNP)/Variant" information available for 2Y3S)

(no "PROSITE Motif" information available for 2Y3S)

(no "Exon" information available for 2Y3S)

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:497
 aligned with D3Y1I2_9ACTN | D3Y1I2 from UniProtKB/TrEMBL  Length:500

    Alignment length:497
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       
         D3Y1I2_9ACTN     4 IDSVAPGDIRYEDLRRGENLRFVGDPEEIHLVGSAAEIEQVLSRAVRSGKRVAVRSGGHCYEDFVANSDVRVVMDMSRLSAVGFDEERGAFAVEAGATLGAVYKTLFRVWGVTLPGGACPDVGAGGHILGGGYGPLSRMHGSIVDYLHAVEVVVVDASGDARTVIATREPSDPNHDLWWAHTGGGGGNFGVVVRYWLRTAEADVPPEPGRLLPRPPAEVLLNTTVWPWEGLDEAAFARLVRNHGRWFEQNSGPDSPWCDLYSVLALTRSQSGALAMTTQLDATGPDAEKRLETYLAAVSEGVGVQPHSDTRRLPWLHSTRWPGIAGDGDMTGRAKIKAAYARRSFDDRQIGTLYTRLTSTDYDNPAGVVALIAYGGKVNAVPADRTAVAQRDSILKIVYVTTWEDPAQDPVHVRWIRELYRDVYADTGGVPVPGGAADGAYVNYPDVDLADEEWNTSGVPWSELYYKDAYPRLQAVKARWDPRNVFRHALSVRVPPA 500
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....hhhhhh............eeee..hhhhhhhhhhhhhhh...eeee................eeee......eeee....eeeee...hhhhhhhhhhhhhh...........hhhhhhhh.....hhhhhhhhhh.eeeeeeeee.....eeeeeee......hhhhhhhh.........eeeeeee.........hhhhh......eeeeeeeeee....hhhhhhhhhhhhhhhhhhh....hhhh.eeeeeeee.hhh.eeeeeeeee....hhhhhhhhhhhhhhh......eeeeeeeehhhhh.hhhhhh......eeeeeeeee....hhhhhhhhhhhhhh........eeeeee.hhhhhhh.............eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.................hhhhhh........hhhhhhhh.hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y3s A   4 IDSVAPGDIRYEDLRRGENLRFVGDPEEIHLVGSAAEIEQVLSRAVRSGKRVAVRSGGHCYEDFVANSDVRVVMDMSRLSAVGFDEERGAFAVEAGATLGAVYKTLFRVWGVTLPGGACPDVGAGGHILGGGYGPLSRMHGSIVDYLHAVEVVVVDASGDARTVIATREPSDPNHDLWWAHTGGGGGNFGVVVRYWLRTAEADVPPEPGRLLPRPPAEVLLNTTVWPWEGLDEAAFARLVRNHGRWFEQNSGPDSPWCDLYSVLALTRSQSGALAMTTQLDATGPDAEKRLETYLAAVSEGVGVQPHSDTRRLPWLHSTRWPGIAGDGDMTGRAKIKAAYARRSFDDRQIGTLYTRLTSTDYDNPAGVVALIAYGGKVNAVPADRTAVAQRDSILKIVYVTTWEDPAQDPVHVRWIRELYRDVYADTGGVPVPGGAADGAYVNYPDVDLADEEWNTSGVPWSELYYKDAYPRLQAVKARWDPRNVFRHALSVRVPPA 500
                                    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       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493

Chain B from PDB  Type:PROTEIN  Length:493
 aligned with D3Y1I2_9ACTN | D3Y1I2 from UniProtKB/TrEMBL  Length:500

    Alignment length:498
                                    12        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       362       372       382       392       402       412       422       432       442       452       462       472       482       492        
         D3Y1I2_9ACTN     3 HIDSVAPGDIRYEDLRRGENLRFVGDPEEIHLVGSAAEIEQVLSRAVRSGKRVAVRSGGHCYEDFVANSDVRVVMDMSRLSAVGFDEERGAFAVEAGATLGAVYKTLFRVWGVTLPGGACPDVGAGGHILGGGYGPLSRMHGSIVDYLHAVEVVVVDASGDARTVIATREPSDPNHDLWWAHTGGGGGNFGVVVRYWLRTAEADVPPEPGRLLPRPPAEVLLNTTVWPWEGLDEAAFARLVRNHGRWFEQNSGPDSPWCDLYSVLALTRSQSGALAMTTQLDATGPDAEKRLETYLAAVSEGVGVQPHSDTRRLPWLHSTRWPGIAGDGDMTGRAKIKAAYARRSFDDRQIGTLYTRLTSTDYDNPAGVVALIAYGGKVNAVPADRTAVAQRDSILKIVYVTTWEDPAQDPVHVRWIRELYRDVYADTGGVPVPGGAADGAYVNYPDVDLADEEWNTSGVPWSELYYKDAYPRLQAVKARWDPRNVFRHALSVRVPPA 500
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.....hhhhhh............eeee..hhhhhhhhhhhhhhhh..eeee................eeee......eeee....eeeee...hhhhhhhhhhhhhh...........hhhhhhhh.....hhhhhhhhhh.eeeeeeeee.....eeeeeee......hhhhhhhh.........eeeeeee....-----hhhhh......eeeeeeeeee....hhhhhhhhhhhhhhhhhhh....hhhh.eeeeeeee.hhh.eeeeeeeee....hhhhhhhhhhhhhhh......eeeeeeeehhhhh.hhhhhh......eeeeeeeee....hhhhhhhhhhhhhh.......eeeeeee.hhhhhhh.............eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh.................hhhhhh........hhhhhhhh.hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y3s B   3 HIDSVAPGDIRYEDLRRGENLRFVGDPEEIHLVGSAAEIEQVLSRAVRSGKRVAVRSGGHCYEDFVANSDVRVVMDMSRLSAVGFDEERGAFAVEAGATLGAVYKTLFRVWGVTLPGGACPDVGAGGHILGGGYGPLSRMHGSIVDYLHAVEVVVVDASGDARTVIATREPSDPNHDLWWAHTGGGGGNFGVVVRYWLRTAE-----EPGRLLPRPPAEVLLNTTVWPWEGLDEAAFARLVRNHGRWFEQNSGPDSPWCDLYSVLALTRSQSGALAMTTQLDATGPDAEKRLETYLAAVSEGVGVQPHSDTRRLPWLHSTRWPGIAGDGDMTGRAKIKAAYARRSFDDRQIGTLYTRLTSTDYDNPAGVVALIAYGGKVNAVPADRTAVAQRDSILKIVYVTTWEDPAQDPVHVRWIRELYRDVYADTGGVPVPGGAADGAYVNYPDVDLADEEWNTSGVPWSELYYKDAYPRLQAVKARWDPRNVFRHALSVRVPPA 500
                                    12        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       362       372       382       392       402       412       422       432       442       452       462       472       482       492        
                                                                                                                                                                                                                                   204   210

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 '\|'

(no "SCOP Domain" information available for 2Y3S)

(no "CATH Domain" information available for 2Y3S)

(no "Pfam Domain" information available for 2Y3S)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (D3Y1I2_9ACTN | D3Y1I2)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y3s)

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	2y3s
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	D3Y1I2_9ACTN \| D3Y1I2	:	2y08 2y3r 2y4g

2y08	STRUCTURE OF THE SUBSTRATE-FREE FAD-DEPENDENT TIRANDAMYCIN OXIDASE TAML
2y3r	STRUCTURE OF THE TIRANDAMYCIN-BOUND FAD-DEPENDENT TIRANDAMYCIN OXIDASE TAML IN P21 SPACE GROUP
2y4g	STRUCTURE OF THE TIRANDAMYCIN-BOUND FAD-DEPENDENT TIRANDAMYCIN OXIDASE TAML IN P212121 SPACE GROUP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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