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Title :   CRYSTAL STRUCTURE OF P-HYDROXYBENZOATE HYDROXYLASE RECONSTITUTED WITH THE MODIFIED FAD PRESENT IN ALCOHOL OXIDASE FROM METHYLOTROPHIC YEASTS: EVIDENCE FOR AN ARABINOFLAVIN

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

Date :   01 Dec 94 (Deposition) - 31 Mar 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

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

Reference :   W. J. Van Berkel, M. H. Eppink, H. A. Schreuder
Crystal Structure Of P-Hydroxybenzoate Hydroxylase Reconstituted With The Modified Fad Present In Alcohol Oxidase From Methylotrophic Yeasts: Evidence For An Arabinoflavin.
Protein Sci. V. 3 2245 1994
PubMed-ID: 7756982
(for further references see the PDB file header)

Molecule 1 - P-HYDROXYBENZOATE HYDROXYLASE
	Chains	:	A
	EC Number	:	1.14.13.2
	Engineered	:	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	FAS	1	Ligand/Ion	ARABINO-FLAVIN-ADENINE DINUCLEOTIDE
2	PHB	1	Ligand/Ion	P-HYDROXYBENZOIC ACID

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	FAS	2	Ligand/Ion	ARABINO-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 , GLU A:32 , ARG A:33 , ARG A:42 , ARG A:44 , ALA A:45 , GLN A:102 , CYS A:158 , ASP A:159 , GLY A:160 , GLY A:163 , ILE A:164 , TYR A:222 , GLY A:285 , ASP A:286 , PRO A:293 , ALA A:296 , GLY A:298 , LEU A:299 , PHB A:396 , HOH A:399 , HOH A:400 , HOH A:401 , HOH A:407 , HOH A:493 , HOH A:495 , HOH A:501 , HOH A:505 , HOH A:506 , HOH A:545 , HOH A:555 , HOH A:622	BINDING SITE FOR RESIDUE FAS A 395
2	AC2	SOFTWARE	ARG A:44 , TRP A:185 , TYR A:201 , LEU A:210 , SER A:212 , ARG A:214 , TYR A:222 , PRO A:293 , THR A:294 , ALA A:296 , FAS A:395	BINDING SITE FOR RESIDUE PHB A 396

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 1PDH)

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 d1pdha1 A:1-173,A:276-391 p-Hydroxybenzoate hydroxylase, PHBH                                                                                                                d1pdha2 A:174-275 p-Hydroxybenzoate hydroxylase (PHBH)                                                d1pdha1 A:1-173,A:276-391 p-Hydroxybenzoate hydroxylase, PHBH                                                        SCOP domains
               CATH domains 1pdhA01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]   1pdhA02                1pdhA01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]                1pdhA02 A:73-95,A:181-268,A:352-388 D-Amino Acid Oxidase, subunit A, domain 2           1pdhA01 A:1-72,A:96-180,A:269-351  [code=3.50.50.60, no name defined]              1pdhA02 A:73-95,A:181-268,A:352-388  --- CATH domains
               Pfam domains -FAD_binding_3-1pdhA01 A:2-343                                                                                                                                                                                                                                                                                                                         ------------------------------------------------ Pfam domains
         Sec.struct. author .ee.eeee...hhhhhhhhhhhh....eeee....hhhhh......ee.hhhhhhhhh....hhhhhh.eee.eeeeee..eeeeeehhhhh....eee..hhhhhhhhhhhhhhh..eee...eeeeee.......eeeeee..eeeeee..eeee......hhhh...hhh.eeeeeeeeeeeeeeee.........eee......eeeeeee..eeeeeeeee....hhh..hhhhhhhhhhh..hhhh.......eeeeeeeeeeeeeee..ee..eee.hhh.ee..hhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdh A   1 MKTQVAIIGAGPSGLLLGQLLHKAGIDNVILERQTPDYVLGRIRAGVLEQGMVDLLREAGVDRRMARDGLVHEGVEIAFAGQRRRIDLKRLSGGKTVTVYGQTEVTRDLMEAREACGATTVYQAAEVRLHDLQGERPYVTFERDGERLRLDCDYIAGCDGFHGISRQSIPAERLKVFERVYPFGWLGLLADTPPVSHELIYANHPRGFALCSQRSATRSRYYVQVPLTEKVEDWSDERFWTELKARLPAEVAEKLVTGPSLEKSIAPLRSFVVEPMQHGRLFLAGDAAHIVPPTGAKGLNLAASDVSTLYRLLLKAYREGRGELLERYSAICLRRIWKAERFSWWMTSVLHRFPDTDAFSQRIQQTELEYYLGSEAGLATIAENYVGLPYE 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( (-)

)

Homologous Superfamilies( (-)

)

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 (8)

1pdhA02

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 (9)

1pdhA01

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: FAD_binding_3 (21)

Pseudomonas fluorescens (7)

FAD_binding_3-1pdhA01

A:2-343

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

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	1pdh
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SS Bonds (0, 0)

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