1BF3 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   P-HYDROXYBENZOATE HYDROXYLASE (PHBH) MUTANT WITH CYS 116 REPLACED BY SER (C116S) AND ARG 42 REPLACED BY LYS (R42K), IN COMPLEX WITH FAD AND 4-HYDROXYBENZOIC ACID

Authors :   M. H. M. Eppink, H. A. Schreuder, W. J. H. Van Berkel

Date :   26 May 98 (Deposition) - 12 Aug 98 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Reference :   M. H. Eppink, H. A. Schreuder, W. J. Van Berkel
Lys42 And Ser42 Variants Of P-Hydroxybenzoate Hydroxylase From Pseudomonas Fluorescens Reveal That Arg42 Is Essential For Nadph Binding.
Eur. J. Biochem. V. 253 194 1998
PubMed-ID: 9578477 | Reference-DOI: 10.1046/J.1432-1327.1998.2530194.X
(for further references see the PDB file header)

Molecule 1 - P-HYDROXYBENZOATE HYDROXYLASE
	Chains	:	A
	EC Number	:	1.14.13.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	POBA
	Expression System Plasmid	:	PUC9
	Expression System Strain	:	TG2
	Expression System Taxid	:	562
	Expression System Vector	:	LACZ
	Expression System Vector Type	:	PLASMID
	Gene	:	POBA
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	294

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	PHB	1	Ligand/Ion	P-HYDROXYBENZOIC ACID

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	PHB	2	Ligand/Ion	P-HYDROXYBENZOIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:9 , GLY A:11 , PRO A:12 , SER A:13 , LEU A:31 , GLU A:32 , ARG A:33 , GLN A:34 , ARG A:44 , ALA A:45 , GLY A:46 , VAL A:47 , GLN A:102 , CYS A:158 , ASP A:159 , GLY A:160 , GLY A:285 , ASP A:286 , ALA A:296 , LYS A:297 , GLY A:298 , LEU A:299 , ASN A:300 , PHB A:396 , HOH A:400 , HOH A:402 , HOH A:411 , HOH A:521 , HOH A:523 , HOH A:530 , HOH A:537 , HOH A:645Z	BINDING SITE FOR RESIDUE FAD A 395
2	AC2	SOFTWARE	ARG A:44 , VAL A:47 , TRP A:185 , TYR A:201 , SER A:212 , ARG A:214 , TYR A:222 , PRO A:293 , THR A:294 , FAD A:395	BINDING SITE FOR RESIDUE PHB A 396

(no "SS Bond" information available for 1BF3)

Asymmetric Unit

No.	Residues
1	Glu A:274	-	Pro A:275

(no "SAP(SNP)/Variant" information available for 1BF3)

(no "PROSITE Motif" information available for 1BF3)

(no "Exon" information available for 1BF3)

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:391
 aligned with PHHY_PSEFL | P00438 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:391
                                    10        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       360       370       380       390 
           PHHY_PSEFL     1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFWTELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYE 391
               SCOP domains d1bf3a1 A:1-173,A:276-391 p-Hydroxybenzoate hydroxylase, PHBH                                                                                                                d1bf3a2 A:174-275 p-Hydroxybenzoate hydroxylase (PHBH)                                                d1bf3a1 A:1-173,A:276-391 p-Hydroxybenzoate hydroxylase, PHBH                                                        SCOP domains
               CATH domains 1bf3A01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]   1bf3A02                1bf3A01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]                1bf3A02 A:73-95,A:181-268,A:352-388 D-Amino Acid Oxidase, subunit A, domain 2           1bf3A01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]              1bf3A02 A:73-95,A:181-268,A:352-388  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eeee...hhhhhhhhhhhh....eeee....hhhhh......eeehhhhhhhhh....hhhhhh.eee.eeeeee..eeeeeehhhh.....eee..hhhhhhhhhhhhhhh..eee...eeeeee.......eeeeee..eeeeee..eeee......hhhh...hhh.eeeeeeeeeeeeeeee.........eeee.....eeeeeee..eeeeeeee.....hhh..hhhhhhhhhhh..hhhhhh.....eeeeeeeeeeeeeee..ee..eee.hhh.ee..hhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bf3 A   1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGKIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREASGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFWTELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYE 391
                                    10        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       360       370       380       390

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-Amino Acid Oxidase; Chain A, domain 2 (80)

Homologous Superfamily: D-Amino Acid Oxidase, subunit A, domain 2 (80)

Pseudomonas fluorescens. Organism_taxid: 294. (6)

1bf3A02

A:73-95,A:181-268,A:352-388

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Pseudomonas fluorescens. Organism_taxid: 294. (6)

1bf3A01

A:1-72,A:96-180,A:269-351

(no "Pfam Domain" information available for 1BF3)

Asymmetric Unit(hide GO term definitions)

Chain A (PHHY_PSEFL | P00438)

molecular function
	GO:0018659	4-hydroxybenzoate 3-monooxygenase activity	Catalysis of the reaction: 4-hydroxybenzoate + NADPH + H+ + O2 = protocatechuate + NADP+ + H2O.
	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: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: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:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0043639	benzoate catabolic process	The chemical reactions and pathways resulting in the breakdown of benzoate, the anion of benzoic acid (benzenecarboxylic acid), a fungistatic compound widely used as a food preservative; it is conjugated to glycine in the liver and excreted as hippuric acid.
	GO:0043640	benzoate catabolic process via hydroxylation	The chemical reactions and pathways resulting in the breakdown of benzoate, by its hydroxylation to cis-1,2-dihydroxybenzoate followed by dehydrogenation to catechol.
	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
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PHB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:274 - Pro A:275	[ RasMol ]

Biological Unit
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Access by PDB/NDB ID
	1bf3
		Family and Domain Information	:	ProDom \| SYSTERS
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	PHHY_PSEFL \| P00438
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	1.14.13.2
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(no "Related Entries Specified in the PDB File" available for 1BF3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

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 (2, 2)

CATH Domains (2, 2)

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Gene Ontology (9, 9)

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