3N20 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF TOLUENE/O-XYLENE MONOOXYGENASE HYDROXYLASE T201V MUTANT

Authors :   M. S. Mccormick, M. H. Sazinsky, S. J. Lippard

Date :   17 May 10 (Deposition) - 13 Oct 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Diiron, 4-Helix Bundle, Carboxylate Bridge, Metalloenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. J. Song, M. S. Mccormick, R. K. Behan, M. H. Sazinsky, W. Jiang, J. Lin C. Krebs, S. J. Lippard
Active Site Threonine Facilitates Proton Transfer During Dioxygen Activation At The Diiron Center Of Toluene/O-Xylen Monooxygenase Hydroxylase.
J. Am. Chem. Soc. V. 132 13582 2010
PubMed-ID: 20839885 | Reference-DOI: 10.1021/JA1063795

Molecule 1 - TOLUENE O-XYLENE MONOOXYGENASE COMPONENT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET22B(+)
	Fragment	:	ALPHA SUBUNIT
	Gene	:	TOUA
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	320855
	Strain	:	OX1
	Synonym	:	TOLUENE/O-XYLENE MONOOXYGENASE ALPHA SUBUNIT

Molecule 2 - TOLUENE O-XYLENE MONOOXYGENASE COMPONENT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET22B(+)
	Gene	:	TOUE
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	320855
	Strain	:	OX1
	Synonym	:	TOLUENE/O-XYLENE MONOOXYGENASE BETA SUBUNIT

Molecule 3 - TOLUENE O-XYLENE MONOOXYGENASE COMPONENT
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET22B(+)
	Gene	:	TOUB
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	320855
	Strain	:	OX1
	Synonym	:	TOLUENE/O-XYLENE MONOOXYGENASE GAMMA SUBUNIT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	FE	2	Ligand/Ion	FE (III) ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	P6G	4	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	P6G	-1	Ligand/Ion	HEXAETHYLENE GLYCOL

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	P6G	4	Ligand/Ion	HEXAETHYLENE GLYCOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:445 , ASN A:446 , ASN B:51	BINDING SITE FOR RESIDUE GOL A 499
02	AC2	SOFTWARE	MET A:93 , PHE A:144 , ASN A:148 , ASP A:217 , HOH A:591 , HOH A:717	BINDING SITE FOR RESIDUE GOL A 500
03	AC3	SOFTWARE	ILE A:100 , GLU A:104 , ALA A:107 , GLU A:134 , PHE A:176 , PHE A:196 , GLU A:197 , GLN A:204 , LEU A:208 , GLU A:231 , LEU A:272 , THR A:273 , ILE A:276 , FE A:505 , FE A:506 , HOH A:507 , HOH A:787	BINDING SITE FOR RESIDUE P6G A 501
04	AC4	SOFTWARE	TRP A:167 , TRP A:338 , PRO A:340 , THR A:341 , LEU A:393 , PRO A:394 , LEU A:464	BINDING SITE FOR RESIDUE P6G A 502
05	AC5	SOFTWARE	LYS A:65 , GLY A:68 , ALA A:69 , ILE A:72 , LEU A:206 , ALA A:209 , SER A:225 , SER A:226 , GLN A:228 , THR A:229	BINDING SITE FOR RESIDUE P6G A 503
06	AC6	SOFTWARE	GLU A:391 , THR A:392 , PHE A:454 , GLN A:460 , ALA A:462 , ASP A:463 , HOH A:651 , HOH A:745 , HOH A:774 , PRO C:20 , HIS C:37	BINDING SITE FOR RESIDUE P6G A 504
07	AC7	SOFTWARE	GLU A:104 , GLU A:134 , HIS A:137 , P6G A:501 , FE A:506 , HOH A:507 , HOH A:509	BINDING SITE FOR RESIDUE FE A 505
08	AC8	SOFTWARE	GLU A:134 , GLU A:197 , GLU A:231 , HIS A:234 , P6G A:501 , FE A:505 , HOH A:507	BINDING SITE FOR RESIDUE FE A 506
09	AC9	SOFTWARE	CYS B:62 , SER B:65 , LEU B:67 , TRP B:72 , TRP B:215 , HOH B:424 , HOH B:428 , HOH B:540	BINDING SITE FOR RESIDUE GOL B 331
10	BC1	SOFTWARE	THR B:39 , ASP B:70 , ASP B:71 , TRP B:72 , ASN B:73 , PRO B:147 , HOH B:424 , HOH B:428	BINDING SITE FOR RESIDUE GOL B 332

(no "SS Bond" information available for 3N20)

Asymmetric Unit

No.	Residues
1	Gln A:460	-	Pro A:461

(no "SAP(SNP)/Variant" information available for 3N20)

(no "PROSITE Motif" information available for 3N20)

(no "Exon" information available for 3N20)

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:491
 aligned with Q6IV66_9PSED | Q6IV66 from UniProtKB/TrEMBL  Length:498

    Alignment length:491
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491 
         Q6IV66_9PSED     2 SMLKREDWYDLTRTTNWTPKYVTENELFPEEMSGARGISMEAWEKYDEPYKITYPEYVSIQREKDSGAYSIKAALERDGFVDRADPGWVSTMQLHFGAIALEEYAASTAEARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMMMTRDSVAVSIMLTFAFETGFTNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVLTGPIMDYYTPLESRNQSFKEFMLEWIVAQFERQLLDLGLDKPWYWDQFMQDLDETHHGMHLGVWYWRPTVWWDPAAGVSPEEREWLEEKYPGWNDTWGQCWDVITDNLVNGKPELTVPETLPTICNMCNLPIAHTPGNKWNVKDYQLEYEGRLYHFGSEADRWCFQIDPERYENHTNLVDRFLKGEIQPADLAGALMYMSLEPGVMGDDAHDYEWVKAYQ 492
               SCOP domains d3n20a_ A: Toluene, o-xylene monooxygenase oxygenase subunit TouA                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Phenol_Hydrox-3n20A01 A:17-251                                                                                                                                                                                                             ---------------------------------------------------------------------------------------------------------------------------------------------------------YHS-3n20A02 A:405-448                       -------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.........hhhhhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh..................hhhhh......eee..eee...hhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhh.............hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n20 A   2 SMLKREDWYDLTRTTNWTPKYVTENELFPEEMSGARGISMEAWEKYDEPYKITYPEYVSIQREKDSGAYSIKAALERDGFVDRADPGWVSTMQLHFGAIALEEYAASTAEARMARFAKAPGNRNMATFGMMDENRHGQIQLYFPYANVKRSRKWDWAHKAIHTNEWAAIAARSFFDDMMMTRDSVAVSIMLTFAFETGFVNMQFLGLAADAAEAGDHTFASLISSIQTDESRHAQQGGPSLKILVENGKKDEAQQMVDVAIWRSWKLFSVLTGPIMDYYTPLESRNQSFKEFMLEWIVAQFERQLLDLGLDKPWYWDQFMQDLDETHHGMHLGVWYWRPTVWWDPAAGVSPEEREWLEEKYPGWNDTWGQCWDVITDNLVNGKPELTVPETLPTICNMCNLPIAHTPGNKWNVKDYQLEYEGRLYHFGSEADRWCFQIDPERYENHTNLVDRFLKGEIQPADLAGALMYMSLEPGVMGDDAHDYEWVKAYQ 492
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491

Chain B from PDB  Type:PROTEIN  Length:322
 aligned with Q6IV62_9PSED | Q6IV62 from UniProtKB/TrEMBL  Length:330

    Alignment length:322
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  
         Q6IV62_9PSED     8 ALKPLKTWSHLAGNRRRPSEYEVVSTNLHYFTDNPERPWELDSNLPMQTWYKKYCFDSPLKHDDWNAFRDPDQLVYRTYNLLQDGQESYVQGLFDQLNDRGHDQMLTREWVETLARFYTPARYLFHALQMGSVYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANCYPDVGFGKRERDVWENDPAWQGFRELIEKALIAWDWGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGNREVLQKWVAKWEPLADKAIEAYCSALPDGENAIVEAKSASRYVRQMMG 329
               SCOP domains d3n20b_ B: Toluene, o-xylene monooxygenase oxygenase subunit TouE                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------Phenol_Hydrox-3n20B01 B:56-281                                                                                                                                                                                                    ------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhh...hhhhh..........hhhhhhhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n20 B   8 ALKPLKTWSHLAGNRRRPSEYEVVSTNLHYFTDNPERPWELDSNLPMQTWYKKYCFDSPLKHDDWNAFRDPDQLVYRTYNLLQDGQESYVQGLFDQLNDRGHDQMLTREWVETLARFYTPARYLFHALQMGSVYIHQIAPASTITNCATYETADHLRWLTHTAYRTRELANCYPDVGFGKRERDVWENDPAWQGFRELIEKALIAWDWGEAFTAINLVTKPAVEEALLQQLGSLAQSEGDTLLGLLAQAQKRDAERHRRWSSALVKMALEKEGNREVLQKWVAKWEPLADKAIEAYCSALPDGENAIVEAKSASRYVRQMMG 329
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327

Chain C from PDB  Type:PROTEIN  Length:83
 aligned with Q6IV65_9PSED | Q6IV65 from UniProtKB/TrEMBL  Length:86

    Alignment length:83
                                    12        22        32        42        52        62        72        82   
         Q6IV65_9PSED     3 TFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMD  85
               SCOP domains d3n20c_ C: Toluene, o-xylene monooxygenase oxygenase subunit TouB                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains TmoB-3n20C01 C:3-85                                                                 Pfam domains
         Sec.struct. author .eeeeeee......eeeee....hhhhhhhhhhh.............eeeeee.....ee....hhhhh......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                 3n20 C   3 TFPIMSNFERDFVIQLVPVDTEDTMDQVAEKCAYHSINRRVHPQPEKILRVRRHEDGTLFPRGMIVSDAGLRPTETLDIIFMD  85
                                    12        22        32        42        52        62        72        82

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 "CATH Domain" information available for 3N20)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Phenol_Hydrox (21)

Pseudomonas sp. OX1 (4)

1a	Phenol_Hydrox-3n20B01	B:56-281
1b	Phenol_Hydrox-3n20A01	A:17-251

Clan: TRASH (61)

Family: YHS (8)

Pseudomonas sp. OX1 (4)

YHS-3n20A02

A:405-448

Clan: Ubiquitin (279)

Family: TmoB (8)

Pseudomonas sp. OX1 (4)

TmoB-3n20C01

C:3-85

Asymmetric Unit(hide GO term definitions)

Chain A (Q6IV66_9PSED | Q6IV66)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	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.
biological process
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
	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.

Chain B (Q6IV62_9PSED | Q6IV62)

molecular function
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	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:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and one atom of oxygen is incorporated into one donor.
biological process
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
	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.

Chain C (Q6IV65_9PSED | Q6IV65)

molecular function
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
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.

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	Cis Peptide Bonds
		Gln A:460 - Pro A:461	[ RasMol ]

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	3n20
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1t0q	WILD-TYPE FORM OF THE SAME PROTEIN AT 2.15 RESOLUTION
2inc	WILD-TYPE FORM OF THE SAME PROTEIN AT 1.85 RESOLUTION
2ind	MN(II) RECONSTITUTED FORM OF THE SAME PROTEIN WITH NO MUTATIONS
2rdb	THE SAME PROTEIN WITH ILE-100 MUTATED TO TRP IN THE HYDROXYLASE ALPHA SUBUNIT
3n1x
3n1y
3n1z

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (3, 3)

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Pfam Domains (3, 4)

Gene Ontology (6, 12)

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