4BK1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF 3-HYDROXYBENZOATE 6-HYDROXYLASE UNCOVERS LIPID-ASSISTED FLAVOPROTEIN STRATEGY FOR REGIOSELECTIVE AROMATIC HYDROXYLATION: H213S MUTANT IN COMPLEX WITH 3-HYDROXYBENZOATE

Authors :   R. Orru, S. Montersino, A. Barendregt, A. H. Westphal, E. Van Duijn, A. W. J. H. Van Berkel

Date :   21 Apr 13 (Deposition) - 24 Jul 13 (Release) - 25 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Oxidoreductase, Flavoprotein, Gentisate, Hydroxylase, Monooxygenase, Phospholipid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Montersino, R. Orru, A. Barendregt, A. H. Westphal, E. Van Duijn, A. Mattevi, W. J. H. Van Berkel
Crystal Structure Of 3-Hydroxybenzoate 6-Hydroxylase Uncovers Lipid-Assisted Flavoprotein Strategy For Regioselective Aromatic Hydroxylation
J. Biol. Chem. V. 288 26235 2013
PubMed-ID: 23864660 | Reference-DOI: 10.1074/JBC.M113.479303

Molecule 1 - PROBABLE SALICYLATE MONOOXYGENASE
	Chains	:	A
	EC Number	:	1.14.13.1, 1.14.13.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	RHODOCOCCUS JOSTII
	Organism Taxid	:	101510
	Strain	:	RHA1
	Synonym	:	3-HYDROXYBENZOATE 6-HYDROXYLASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	3HB	1	Ligand/Ion	3-HYDROXYBENZOIC ACID
2	CL	1	Ligand/Ion	CHLORIDE ION
3	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	P3A	1	Ligand/Ion	PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	3HB	2	Ligand/Ion	3-HYDROXYBENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	P3A	2	Ligand/Ion	PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:13 , GLY A:15 , ILE A:16 , GLY A:17 , PHE A:35 , GLU A:36 , ARG A:37 , LEU A:48 , GLN A:49 , ARG A:110 , THR A:133 , VAL A:134 , MET A:162 , ASP A:163 , GLY A:164 , ARG A:187 , GLY A:293 , ASP A:294 , GLN A:301 , ALA A:304 , SER A:305 , GLY A:306 , ALA A:307 , VAL A:308 , 3HB A:1400 , CL A:1401 , HOH A:2007 , HOH A:2008 , HOH A:2038 , HOH A:2165 , HOH A:2166 , HOH A:2169 , HOH A:2365 , HOH A:2366 , HOH A:2367 , HOH A:2368	BINDING SITE FOR RESIDUE FAD A1398
2	AC2	SOFTWARE	GLN A:49 , TYR A:105 , ARG A:350 , THR A:354 , MET A:357 , TRP A:358 , LEU A:361 , GLU A:374 , LYS A:385 , TYR A:386 , TRP A:389 , HOH A:2298 , HOH A:2349 , HOH A:2356	BINDING SITE FOR RESIDUE P3A A1399
3	AC3	SOFTWARE	GLN A:49 , ILE A:215 , TYR A:217 , VAL A:230 , GLN A:301 , FAD A:1398 , HOH A:2037	BINDING SITE FOR RESIDUE 3HB A1400
4	AC4	SOFTWARE	GLN A:301 , SER A:305 , GLY A:306 , FAD A:1398 , HOH A:2270	BINDING SITE FOR RESIDUE CL A1401

(no "SS Bond" information available for 4BK1)

(no "Cis Peptide Bond" information available for 4BK1)

(no "SAP(SNP)/Variant" information available for 4BK1)

(no "PROSITE Motif" information available for 4BK1)

(no "Exon" information available for 4BK1)

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:389
 aligned with Q0SFK6_RHOJR | Q0SFK6 from UniProtKB/TrEMBL  Length:399

    Alignment length:395
                                    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     
         Q0SFK6_RHOJR     3 NLQDARIIIAGGGIGGAANALALAQKGANVTLFERASEFGEVGAGLQVGPHGARILDSWGVLDDVLSRAFLPKNIVFRDAITAEVLTKIDLGSEFRGRYGGPYFVTHRSDLHATLVDAARAAGAELHTGVTVTDVITEGDKAIVSTDDGRTHEADIALGMDGLKSRLREKISGDEPVSSGYAAYRGTTPYRDVELDEDIEDVVGYIGPRCHFIQYPLRGGEMLNQVAVFESPGFKNGIENWGGPEELEQAYAHCHENVRRGIDYLWKDRWWPMYDREPIENWVDGRMILLGDAAHPPLQYLASGAVMAIEDAKCLADYAAEDFSTGGNSAWPQILKEVNTERAPRCNRILTTGRMWGELWHLDGTARIARNELFRTRDTSSYKYTDWLWGYSSDR 397
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeeee..........eeeehhhhhhhhhhh.hhhhhhh......eeeeee.....eeeeee.hhhhhhhhh...eeeehhhhhhhhhhhhhhh..eeee...eeeeeee..eeeeee....eeee.eeee......hhhhhh.....eeeeeeeeeeeee.------.....eeeeee..eeeeeeeehhh.eeeeeeeeehhhhhhh.....hhhhhhhhh...hhhhhhhhh.......eeeee.......ee..eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bk1 A   3 NLQDARIIIAGGGIGGAANALALAQKGANVTLFERASEFGEVGAGLQVGPHGARILDSWGVLDDVLSRAFLPKNIVFRDAITAEVLTKIDLGSEFRGRYGGPYFVTHRSDLHATLVDAARAAGAELHTGVTVTDVITEGDKAIVSTDDGRTHEADIALGMDGLKSRLREKISGDEPVSSGYAAYRGTTPY------EDIEDVVGYIGPRCSFIQYPLRGGEMLNQVAVFESPGFKNGIENWGGPEELEQAYAHCHENVRRGIDYLWKDRWWPMYDREPIENWVDGRMILLGDAAHPPLQYLASGAVMAIEDAKCLADYAAEDFSTGGNSAWPQILKEVNTERAPRCNRILTTGRMWGELWHLDGTARIARNELFRTRDTSSYKYTDWLWGYSSDR 397
                                    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     
                                                                                                                                                                                                                       192    199

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 4BK1)

(no "CATH Domain" information available for 4BK1)

(no "Pfam Domain" information available for 4BK1)

Asymmetric Unit(hide GO term definitions)

Chain A (Q0SFK6_RHOJR | Q0SFK6)

molecular function
	GO:0071949	FAD binding	Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	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: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:0018658	salicylate 1-monooxygenase activity	Catalysis of the reaction: salicylate + NADH + H+ + O2 = catechol + NAD+ + H2O + CO2.
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 Unit
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	Ligands, Modified Residues, Ions
		3HB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		P3A	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bk1)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
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	4bk1
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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Access by UniProt ID/Accession number
	Q0SFK6_RHOJR \| Q0SFK6
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Access by Enzyme Classificator (EC Number)
	1.14.13.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	1.14.13.24
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	Q0SFK6_RHOJR \| Q0SFK6
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UniProtKB/TrEMBL
	Q0SFK6_RHOJR \| Q0SFK6	:	4bjy 4bjz 4bk2 4bk3 5hym

4bjy	CRYSTAL STRUCTURE OF 3-HYDROXYBENZOATE 6-HYDROXYLASE UNCOVERS LIPID-ASSISTED FLAVOPROTEIN STRATEGY FOR REGIOSELECTIVE AROMATIC HYDROXYLATION: PLATINUM DERIVATIVE
4bjz	CRYSTAL STRUCTURE OF 3-HYDROXYBENZOATE 6-HYDROXYLASE UNCOVERS LIPID-ASSISTED FLAVOPROTEIN STRATEGY FOR REGIOSELECTIVE AROMATIC HYDROXYLATION: NATIVE DATA
4bk2	CRYSTAL STRUCTURE OF 3-HYDROXYBENZOATE 6-HYDROXYLASE UNCOVERS LIPID-ASSISTED FLAVOPROTEIN STRATEGY FOR REGIOSELECTIVE AROMATIC HYDROXYLATION: Q301E MUTANT
4bk3	CRYSTAL STRUCTURE OF 3-HYDROXYBENZOATE 6-HYDROXYLASE UNCOVERS LIPID-ASSISTED FLAVOPROTEIN STRATEGY FOR REGIOSELECTIVE AROMATIC HYDROXYLATION: Y105F MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

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

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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