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Title :   STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH ISOEUGENOL

Authors :   A. Mattevi

Date :   10 Apr 97 (Deposition) - 15 Oct 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (4x)

Keywords :   Flavoenzyme, Oxidase, Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Mattevi, M. W. Fraaije, A. Mozzarelli, L. Olivi, A. Coda, W. J. Van Berkel
Crystal Structures And Inhibitor Binding In The Octameric Flavoenzyme Vanillyl-Alcohol Oxidase: The Shape Of The Active-Site Cavity Controls Substrate Specificity.
Structure V. 5 907 1997
PubMed-ID: 9261083 | Reference-DOI: 10.1016/S0969-2126(97)00245-1
(for further references see the PDB file header)

Molecule 1 - VANILLYL-ALCOHOL OXIDASE
	Atcc	:	90172
	Cellular Location	:	INTRACELLULAR
	Chains	:	A, B
	EC Number	:	1.1.3.13
	Organelle	:	PEROXISOMES
	Organism Scientific	:	PENICILLIUM SIMPLICISSIMUM
	Organism Taxid	:	69488
	Other Details	:	COVALENT BOND BETWEEN FAD AND HIS 422
	Other Details - Source	:	FUNGUS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	EUG	2	Ligand/Ion	2-METHOXY-4-VINYL-PHENOL
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	EUG	8	Ligand/Ion	2-METHOXY-4-VINYL-PHENOL
2	FAD	8	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:99 , ILE A:100 , SER A:101 , ILE A:102 , GLY A:103 , ARG A:104 , ASN A:105 , MET A:123 , PRO A:169 , ASP A:170 , LEU A:171 , GLY A:174 , SER A:175 , ASN A:179 , GLU A:182 , GLY A:184 , VAL A:185 , TYR A:187 , VAL A:262 , TRP A:413 , ILE A:414 , HIS A:422 , PHE A:424 , ARG A:504 , EUG A:601 , HOH A:602	BINDING SITE FOR RESIDUE FAD A 600
2	AC2	SOFTWARE	TYR A:108 , ASP A:170 , VAL A:185 , PHE A:424 , HIS A:466 , ILE A:468 , TYR A:503 , ARG A:504 , FAD A:600	BINDING SITE FOR RESIDUE EUG A 601
3	AC3	SOFTWARE	PRO B:99 , ILE B:100 , SER B:101 , ILE B:102 , GLY B:103 , ARG B:104 , ASN B:105 , MET B:123 , PRO B:169 , ASP B:170 , LEU B:171 , GLY B:174 , SER B:175 , ASN B:179 , GLU B:182 , GLY B:184 , VAL B:185 , TYR B:187 , VAL B:262 , TRP B:413 , ILE B:414 , HIS B:422 , PHE B:424 , ARG B:504 , EUG B:601 , HOH B:602	BINDING SITE FOR RESIDUE FAD B 600
4	AC4	SOFTWARE	TYR B:108 , ASP B:170 , VAL B:185 , PHE B:424 , HIS B:466 , ILE B:468 , TYR B:503 , ARG B:504 , FAD B:600	BINDING SITE FOR RESIDUE EUG B 601
5	FAD	UNKNOWN	FAD A:600 , FAD B:600	COFACTOR.

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_PCMH	PS51387	PCMH-type FAD-binding domain profile.	VAOX_PENSI	67-272	2	A:67-272 B:67-272

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FAD_PCMH	PS51387	PCMH-type FAD-binding domain profile.	VAOX_PENSI	67-272	8	A:67-272 B:67-272

(no "Exon" information available for 2VAO)

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:555
 aligned with VAOX_PENSI | P56216 from UniProtKB/Swiss-Prot  Length:560

    Alignment length:555
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555     
           VAOX_PENSI     6 EFRPLTLPPKLSLSDFNEFIQDIIRIVGSENVEVISSKDQIVDGSYMKPTHTHDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLWPISIGRNSGYGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVPDLGGGSVLGNAVERGVGYTPYGDHWMMHSGMEVVLANGELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQSNMGIVTKIGIWLMPNPRGYQSYLITLPKDGDLKQAVDIIRPLRLGMALQNVPTIRHILLDAAVLGDKRSYSSRTEPLSDEELDKIAKQLNLGRWNFYGALYGPEPIRRVLWETIKDAFSAIPGVKFYFPEDTPENSVLRVRDKTMQGIPTYDELKWIDWLPNGAHLFFSPIAKVSGEDAMMQYAVTKKRCQEAGLDFIGTFTVGMREMHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEYRTHLAFMDQIMETYNWNNSSFLRFNEVLKNAVDPNGIIAPGKSGVWPSQYSHVTWKL 560
               SCOP domains d2vaoa2 A:6-273 Vanillyl-alcohol oxidase                                                                                                                                                                                                                                    d2vaoa1 A:274-560 Vanillyl-alcohol oxidase                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2vaoA01 A:6-128 Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2                                       2vaoA02                -------------2vaoA02 A:129-151,A:165-215,A:235-271              -------------------2vaoA02 A:129-151,A:165-215,A:235-271----2vaoA03 A:276-506 Vanillyl-alcohol Oxidase; Chain A, domain 3                                                                                                                                                                          2vaoA04 A:507-559                                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhh.hhheee...hhh.....hhh...................eee....hhhhhhhhhhhhhh...eeee..................eeeehhhh...eeeee....eeee.....hhhhhhhhh...hhh.............hhhhhhh......hhh..hhh...eeeee....eee.hhhh......hhh....hhh..................hhhh.....eeeeeeeee.......eeeeeeee..hhhhhhhhhhhhhhhhh.......eeeehhhhhhhh..............hhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhh....eee.hhh.....hhhhhhhhhh......hhhhhh....eeeeeeeeee...hhhhhhhhhhhhhhhhh......eeeee....eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhh.......hhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------FAD_PCMH  PDB: A:67-272 UniProt: 67-272                                                                                                                                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vao A   6 EFRPLTLPPKLSLSDFNEFIQDIIRIVGSENVEVISSKDQIVDGSYMKPTHTHDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLWPISIGRNSGYGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVPDLGGGSVLGNAVERGVGYTPYGDHWMMHSGMEVVLANGELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQSNMGIVTKIGIWLMPNPRGYQSYLITLPKDGDLKQAVDIIRPLRLGMALQNVPTIRHILLDAAVLGDKRSYSSRTEPLSDEELDKIAKQLNLGRWNFYGALYGPEPIRRVLWETIKDAFSAIPGVKFYFPEDTPENSVLRVRDKTMQGIPTYDELKWIDWLPNGAHLFFSPIAKVSGEDAMMQYAVTKKRCQEAGLDFIGTFTVGMREMHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEYRTHLAFMDQIMETYNWNNSSFLRFNEVLKNAVDPNGIIAPGKSGVWPSQYSHVTWKL 560
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555

Chain B from PDB  Type:PROTEIN  Length:555
 aligned with VAOX_PENSI | P56216 from UniProtKB/Swiss-Prot  Length:560

    Alignment length:555
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555     
           VAOX_PENSI     6 EFRPLTLPPKLSLSDFNEFIQDIIRIVGSENVEVISSKDQIVDGSYMKPTHTHDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLWPISIGRNSGYGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVPDLGGGSVLGNAVERGVGYTPYGDHWMMHSGMEVVLANGELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQSNMGIVTKIGIWLMPNPRGYQSYLITLPKDGDLKQAVDIIRPLRLGMALQNVPTIRHILLDAAVLGDKRSYSSRTEPLSDEELDKIAKQLNLGRWNFYGALYGPEPIRRVLWETIKDAFSAIPGVKFYFPEDTPENSVLRVRDKTMQGIPTYDELKWIDWLPNGAHLFFSPIAKVSGEDAMMQYAVTKKRCQEAGLDFIGTFTVGMREMHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEYRTHLAFMDQIMETYNWNNSSFLRFNEVLKNAVDPNGIIAPGKSGVWPSQYSHVTWKL 560
               SCOP domains d2vaob2 B:6-273 Vanillyl-alcohol oxidase                                                                                                                                                                                                                                    d2vaob1 B:274-560 Vanillyl-alcohol oxidase                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2vaoB01 B:6-128 Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2                                       2vaoB02                -------------2vaoB02 B:129-151,B:165-215,B:235-271              -------------------2vaoB02 B:129-151,B:165-215,B:235-271----2vaoB03 B:276-506 Vanillyl-alcohol Oxidase; Chain A, domain 3                                                                                                                                                                          2vaoB04 B:507-559                                    - CATH domains
           Pfam domains (1) -----------------------------------------------------------------FAD_binding_4-2vaoB03 B:71-213                                                                                                                 --------------------------------------------------------------------------------------------FAD-oxidase_C-2vaoB01 B:306-546                                                                                                                                                                                                                  -------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------FAD_binding_4-2vaoB04 B:71-213                                                                                                                 --------------------------------------------------------------------------------------------FAD-oxidase_C-2vaoB02 B:306-546                                                                                                                                                                                                                  -------------- Pfam domains (2)
         Sec.struct. author ............hhhhhhhhhhhhhhh.hhheee...hhh.....hhh...................eee....hhhhhhhhhhhhhh...eeee..................eeeehhhh...eeeee....eeee.....hhhhhhhhh...hhh.............hhhhhhh......hhh..hhh...eeeee....eee.hhhh......hhh....hhh..................hhhh.....eeeeeeeee.......eeeeeeee..hhhhhhhhhhhhhhhhh.......eeeehhhhhhhh..............hhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhh....eee.hhh.....hhhhhhhhhh......hhhhhh....eeeeeeeeee...hhhhhhhhhhhhhhhhh......eeeee....eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhh.......hhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------FAD_PCMH  PDB: B:67-272 UniProt: 67-272                                                                                                                                                                       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vao B   6 EFRPLTLPPKLSLSDFNEFIQDIIRIVGSENVEVISSKDQIVDGSYMKPTHTHDPHHVMDQDYFLASAIVAPRNVADVQSIVGLANKFSFPLWPISIGRNSGYGGAAPRVSGSVVLDMGKNMNRVLEVNVEGAYCVVEPGVTYHDLHNYLEANNLRDKLWLDVPDLGGGSVLGNAVERGVGYTPYGDHWMMHSGMEVVLANGELLRTGMGALPDPKRPETMGLKPEDQPWSKIAHLFPYGFGPYIDGLFSQSNMGIVTKIGIWLMPNPRGYQSYLITLPKDGDLKQAVDIIRPLRLGMALQNVPTIRHILLDAAVLGDKRSYSSRTEPLSDEELDKIAKQLNLGRWNFYGALYGPEPIRRVLWETIKDAFSAIPGVKFYFPEDTPENSVLRVRDKTMQGIPTYDELKWIDWLPNGAHLFFSPIAKVSGEDAMMQYAVTKKRCQEAGLDFIGTFTVGMREMHHIVCIVFNKKDLIQKRKVQWLMRTLIDDCAANGWGEYRTHLAFMDQIMETYNWNNSSFLRFNEVLKNAVDPNGIIAPGKSGVWPSQYSHVTWKL 560
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD-oxidase_C (26)

Family: FAD-oxidase_C (13)

Penicillium simplicissimum (8)

1a	FAD-oxidase_C-2vaoB01	B:306-546
1b	FAD-oxidase_C-2vaoB02	B:306-546

Clan: FAD_PCMH (53)

Family: FAD_binding_4 (31)

Penicillium simplicissimum (8)

2a	FAD_binding_4-2vaoB03	B:71-213
2b	FAD_binding_4-2vaoB04	B:71-213

Asymmetric Unit(hide GO term definitions)

Chain A,B (VAOX_PENSI | P56216)

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: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.
	GO:0018465	vanillyl-alcohol oxidase activity	Catalysis of the reaction: O(2) + vanillyl alcohol = H(2)O(2) + vanillin.
biological process
	GO:0015945	methanol metabolic process	The chemical reactions and pathways involving methanol, CH3-OH, a colorless, flammable, mobile, poisonous liquid, widely used as a solvent.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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