3KPF - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF THE MUTANT LYS300MET OF POLYAMINE OXIDASE FROM ZEA MAYS

Authors :   A. Fiorillo, A. Ilari, P. Tavladoraki

Date :   16 Nov 09 (Deposition) - 17 Nov 10 (Release) - 17 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Flavoenzyme, Polyamine Oxidase, Disulfide Bond, Fad, Flavoprotein, Glycoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Fiorillo, A. Ilari, P. Tavladoraki
The Crystal Structure Of The Mutant K300M Of Polyamine Oxidase From Zea Mays Unveils The Role Of Lys300 In Catalysis
To Be Published
PubMed: search

Molecule 1 - POLYAMINE OXIDASE
	Chains	:	A, B
	EC Number	:	1.5.3.-
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Strain	:	X-33
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Gene	:	PAO
	Mutation	:	YES
	Organism Common	:	MAIZE
	Organism Scientific	:	ZEA MAYS
	Organism Taxid	:	4577

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 9)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 8)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:10 , GLY A:11 , GLY A:13 , MET A:14 , SER A:15 , LEU A:34 , GLU A:35 , ALA A:36 , THR A:37 , GLY A:42 , ARG A:43 , LEU A:56 , GLY A:57 , ALA A:58 , ASN A:59 , TRP A:60 , LYS A:235 , VAL A:236 , VAL A:237 , SER A:265 , LEU A:275 , ILE A:276 , TYR A:298 , TRP A:393 , PHE A:398 , TYR A:399 , THR A:402 , PHE A:403 , GLY A:429 , GLU A:430 , GLY A:438 , TYR A:439 , VAL A:440 , ALA A:443 , HOH A:483 , HOH A:490 , HOH A:508 , HOH A:509 , HOH A:524 , HOH A:557	BINDING SITE FOR RESIDUE FAD A 500
2	AC2	SOFTWARE	ASN A:65 , TRP A:73 , ASN A:77 , TYR A:197	BINDING SITE FOR RESIDUE NAG A 600
3	AC3	SOFTWARE	ARG A:112	BINDING SITE FOR RESIDUE CL A 479
4	AC4	SOFTWARE	LYS A:46	BINDING SITE FOR RESIDUE ACT A 480
5	AC5	SOFTWARE	VAL B:10 , GLY B:11 , GLY B:13 , MET B:14 , SER B:15 , LEU B:34 , GLU B:35 , ALA B:36 , THR B:37 , GLY B:42 , ARG B:43 , LEU B:56 , GLY B:57 , ALA B:58 , ASN B:59 , TRP B:60 , LYS B:235 , VAL B:237 , SER B:265 , LEU B:275 , TYR B:298 , TRP B:393 , PHE B:398 , TYR B:399 , THR B:402 , PHE B:403 , GLY B:429 , GLU B:430 , GLY B:438 , TYR B:439 , VAL B:440 , ALA B:443 , HOH B:512 , HOH B:542	BINDING SITE FOR RESIDUE FAD B 500
6	AC6	SOFTWARE	ASN B:65 , TRP B:73 , ASN B:77 , TYR B:197 , NAG B:601	BINDING SITE FOR RESIDUE NAG B 600
7	AC7	SOFTWARE	NAG B:600	BINDING SITE FOR RESIDUE NAG B 601
8	AC8	SOFTWARE	ARG B:6 , ASP B:260 , TYR B:261 , ARG B:424 , LYS B:461	BINDING SITE FOR RESIDUE SO4 B 479
9	AC9	SOFTWARE	LYS B:46 , ASN B:53	BINDING SITE FOR RESIDUE ACT B 480

Asymmetric Unit

No.	Residues
1	A:457	-	A:463

Asymmetric Unit

No.	Residues
1	Val A:184	-	Pro A:185
2	Lys A:279	-	Pro A:280
3	Val B:184	-	Pro B:185
4	Lys B:279	-	Pro B:280

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

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

(no "Exon" information available for 3KPF)

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:467
 aligned with PAO_MAIZE | O64411 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:467
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       
            PAO_MAIZE    30 TVGPRVIVVGAGMSGISAAKRLSEAGITDLLILEATDHIGGRMHKTNFAGINVELGANWVEGVNGGKMNPIWPIVNSTLKLRNFRSDFDYLAQNVYKEDGGVYDEDYVQKRIELADSVEEMGEKLSATLHASGRDDMSILAMQRLNEHQPNGPATPVDMVVDYYKFDYEFAEPPRVTSLQNTVPLATFSDFGDDVYFVADQRGYEAVVYYLAGQYLKTDDKSGKIVDPRLQLNKVVREIKYSPGGVTVKTEDNSVYSADYVMVSASLGVLQSDLIQFKPKLPTWKVRAIYQFDMAVYTKIFLKFPRKFWPEGKGREFFLYASSRRGYYGVWQEFEKQYPDANVLLVTVTDEESRRIEQQSDEQTKAEIMQVLRKMFPGKDVPDATDILVPRWWSDRFYKGTFSNWPVGVNRYEYDQLRAPVGRVYFTGEHTSEHYNGYVHGAYLSGIDSAEILINCAQKKMCKYHVQ 496
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh..eeeee...........eeee..eeee....eeeee......hhhhhhhh.....eee....hhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhh.eeeee......hhhhhhhhh................ee....eeeeee....eeeee....eeee.eeee..hhhhhhh...eee...hhhhhhhhhhheee.eeeeeee.............eeeee........eeee.........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.............eee.....hhhhhhhhhh....eee.hhhhh.....hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpf A   2 TVGPRVIVVGAGMSGISAAKRLSEAGITDLLILEATDHIGGRMHKTNFAGINVELGANWVEGVNGGKMNPIWPIVNSTLKLRNFRSDFDYLAQNVYKEDGGVYDEDYVQKRIELADSVEEMGEKLSATLHASGRDDMSILAMQRLNEHQPNGPATPVDMVVDYYKFDYEFAEPPRVTSLQNTVPLATFSDFGDDVYFVADQRGYEAVVYYLAGQYLKTDDKSGKIVDPRLQLNKVVREIKYSPGGVTVKTEDNSVYSADYVMVSASLGVLQSDLIQFKPKLPTWKVRAIYQFDMAVYTMIFLKFPRKFWPEGKGREFFLYASSRRGYYGVWQEFEKQYPDANVLLVTVTDEESRRIEQQSDEQTKAEIMQVLRKMFPGKDVPDATDILVPRWWSDRFYKGTFSNWPVGVNRYEYDQLRAPVGRVYFTGEHTSEHYNGYVHGAYLSGIDSAEILINCAQKKMCKYHVQ 468
                                    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

Chain B from PDB  Type:PROTEIN  Length:464
 aligned with PAO_MAIZE | O64411 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:464
                                    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    
            PAO_MAIZE    32 GPRVIVVGAGMSGISAAKRLSEAGITDLLILEATDHIGGRMHKTNFAGINVELGANWVEGVNGGKMNPIWPIVNSTLKLRNFRSDFDYLAQNVYKEDGGVYDEDYVQKRIELADSVEEMGEKLSATLHASGRDDMSILAMQRLNEHQPNGPATPVDMVVDYYKFDYEFAEPPRVTSLQNTVPLATFSDFGDDVYFVADQRGYEAVVYYLAGQYLKTDDKSGKIVDPRLQLNKVVREIKYSPGGVTVKTEDNSVYSADYVMVSASLGVLQSDLIQFKPKLPTWKVRAIYQFDMAVYTKIFLKFPRKFWPEGKGREFFLYASSRRGYYGVWQEFEKQYPDANVLLVTVTDEESRRIEQQSDEQTKAEIMQVLRKMFPGKDVPDATDILVPRWWSDRFYKGTFSNWPVGVNRYEYDQLRAPVGRVYFTGEHTSEHYNGYVHGAYLSGIDSAEILINCAQKKMCKYHV 495
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Amino_oxidase-3kpfB01 B:14-455                                                                                                                                                                                                                                                                                                                                                                                                                            ------------ Pfam domains (1)
           Pfam domains (2) ----------Amino_oxidase-3kpfB02 B:14-455                                                                                                                                                                                                                                                                                                                                                                                                                            ------------ Pfam domains (2)
         Sec.struct. author ...eeee..hhhhhhhhhhhhhh....eeee...........eeee..eeee....eeeee......hhhhhhhh.....eee....hhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.............hhhhhhhh.eeeee......hhhhhhhhhh...............ee....eeeeee....eeeee....eeee.eeee..hhhhhhh...eee...hhhhhhhhhhheee.eeeeeee.............eeeee........eeee.........eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhh.........eee.............eee.....hhhhhhhhhh....eee.hhhhh.....hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpf B   4 GPRVIVVGAGMSGISAAKRLSEAGITDLLILEATDHIGGRMHKTNFAGINVELGANWVEGVNGGKMNPIWPIVNSTLKLRNFRSDFDYLAQNVYKEDGGVYDEDYVQKRIELADSVEEMGEKLSATLHASGRDDMSILAMQRLNEHQPNGPATPVDMVVDYYKFDYEFAEPPRVTSLQNTVPLATFSDFGDDVYFVADQRGYEAVVYYLAGQYLKTDDKSGKIVDPRLQLNKVVREIKYSPGGVTVKTEDNSVYSADYVMVSASLGVLQSDLIQFKPKLPTWKVRAIYQFDMAVYTMIFLKFPRKFWPEGKGREFFLYASSRRGYYGVWQEFEKQYPDANVLLVTVTDEESRRIEQQSDEQTKAEIMQVLRKMFPGKDVPDATDILVPRWWSDRFYKGTFSNWPVGVNRYEYDQLRAPVGRVYFTGEHTSEHYNGYVHGAYLSGIDSAEILINCAQKKMCKYHV 467
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463

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 3KPF)

(no "CATH Domain" information available for 3KPF)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Amino_oxidase (60)

Zea mays (Maize) (3)

1a	Amino_oxidase-3kpfB01	B:14-455
1b	Amino_oxidase-3kpfB02	B:14-455

Asymmetric Unit(hide GO term definitions)

Chain A,B (PAO_MAIZE | O64411)

molecular function
	GO:0052898	N1-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity	Catalysis of the reaction: H(2)O + N(1)-acetylspermidine + O(2) = 1,3-diaminopropane + 4-acetamidobutanal + H(2)O(2).
	GO:0052893	N1-acetylspermine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity	Catalysis of the reaction: N1-acetylspermine + oxygen + H2O = N-(3-acetamidopropyl)-4-aminobutanal + propane-1,3-diamine + hydrogen peroxide.
	GO:0052897	N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity	Catalysis of the reaction: H(2)O + N(8)-acetylspermidine + O(2) = 1,3-diaminopropane + 4-acetamidobutanal + H(2)O(2).
	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:0052896	spermidine oxidase (propane-1,3-diamine-forming) activity	Catalysis of the reaction: H(2)O + O(2) + spermidine = 1,3-diaminopropane + 4-aminobutanal + H(2)O(2).
	GO:0052900	spermine oxidase (propane-1,3-diamine-forming) activity	Catalysis of the reaction: H(2)O + O(2) + spermine = 1,3-diaminopropane + H(2)O(2) + N-(3-aminopropyl)-4-aminobutanal.
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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Lys A:279 - Pro A:280	[ RasMol ]
		Lys B:279 - Pro B:280	[ RasMol ]
		Val A:184 - Pro A:185	[ RasMol ]
		Val B:184 - Pro B:185	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Access by PDB/NDB ID
	3kpf
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	1.5.3.-
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UniProtKB/Swiss-Prot
	PAO_MAIZE \| O64411	:	1b37 1b5q 1h81 1h82 1h83 1h84 1h86 3ku9 3l1r

1b37	ZMPAO WT
3ku9	ZMPAO K300M IN COMPLEX WITH SPERMINE
3l1r	ZMPAO K300M IN COMPLEX WITH SPERMIDINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (9, 9)

SS Bonds (1, 1)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (7, 7)

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