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Title :   CRYSTAL STRUCTURE OF FMS1 IN COMPLEX WITH S-BZ-MESPERMIDINE

Authors :   Q. Huang, H. Hao

Date :   26 Mar 08 (Deposition) - 22 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Fms1, Polyamine Oxidase, N1-Benzoyl-1-Methylspermidine, Complex, Crystal Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Huang, H. Hao
Crystal Structure Of Fms1 In Complex With S-Bz-Mespermidine
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - FMS1
	Chains	:	A, B
	EC Number	:	1.5.3.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FMS1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	FENPROPIMORPH RESISTANCE MULTICOPY SUPPRESSOR 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SP8	2	Ligand/Ion	N-{(1S)-3-[(4-AMINOBUTYL)AMINO]-1-METHYLPROPYL}BENZAMIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:14 , GLY A:15 , GLY A:17 , ILE A:18 , ALA A:19 , LEU A:38 , GLU A:39 , ALA A:40 , ARG A:41 , GLY A:45 , GLY A:46 , ARG A:47 , GLY A:62 , ALA A:63 , SER A:64 , TRP A:65 , HIS A:67 , CYS A:221 , THR A:252 , PRO A:254 , GLY A:270 , LEU A:294 , TRP A:440 , TYR A:445 , ALA A:449 , TYR A:450 , GLY A:478 , GLU A:479 , GLY A:487 , CYS A:488 , ALA A:489 , ALA A:492	BINDING SITE FOR RESIDUE FAD A 517
2	AC2	SOFTWARE	GLY B:15 , GLY B:17 , ILE B:18 , ALA B:19 , LEU B:38 , GLU B:39 , ALA B:40 , ARG B:41 , GLY B:46 , ARG B:47 , GLY B:62 , ALA B:63 , SER B:64 , TRP B:65 , HIS B:67 , CYS B:221 , THR B:252 , PRO B:254 , GLY B:270 , LEU B:294 , TRP B:440 , TYR B:445 , ALA B:449 , TYR B:450 , GLY B:478 , GLU B:479 , GLY B:487 , CYS B:488 , ALA B:489 , ALA B:492	BINDING SITE FOR RESIDUE FAD B 517
3	AC3	SOFTWARE	TRP A:65 , HIS A:67 , ASP A:94 , LEU A:173 , TRP A:174 , LEU A:294 , LYS A:312 , LEU A:375 , TYR A:450	BINDING SITE FOR RESIDUE SP8 A 518
4	AC4	SOFTWARE	TRP B:65 , HIS B:67 , LEU B:173 , TRP B:174 , LEU B:294 , LEU B:375 , TYR B:450 , GLY B:487	BINDING SITE FOR RESIDUE SP8 B 518

Asymmetric/Biological Unit

No.	Residues
1	A:221	-	A:238
2	B:221	-	B:238

Asymmetric/Biological Unit

No.	Residues
1	Gln A:275	-	Pro A:276
2	Ala A:378	-	Pro A:379
3	Gln B:275	-	Pro B:276
4	Ala B:378	-	Pro B:379

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

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

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YMR020W	1	YMR020W.1	XIII:315376-316902	1527	FMS1_YEAST	1-508	508	2	A:6-508 (gaps) B:9-508 (gaps)	503 500

Asymmetric/Biological 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:492
 aligned with FMS1_YEAST | P50264 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                508 
                                    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  | 
           FMS1_YEAST     6 PAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLK-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3cnsA01 A:6-91,A:196-289,A:445-509  [code=3.50.50.60, no name defined]                3cnsA02 A:92-195,A:290-444  [code=3.90.660.10, no name defined]                                         3cnsA01 A:6-91,A:196-289,A:445-509  [code=3.50.50.60, no name defined]                        3cnsA02 A:92-195,A:290-444  [code=3.90.660.10, no nam      e defined]                                                                                      3cnsA01 A:6-91,A:196-289,A:445-509                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh....eeee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh.......eee..hhhhhhhhhhhhhhh.ee....eeeeeee...eeeeee....eeeeeeeee..hhhhhhhhhh.........eee...hhhhhhhhhhheee..eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhhhh------.........eeeeehhhhhh..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee....------....eeeeeee............eee......hhhhhhhhhh.....eee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:6-508 (gaps) UniProt: 1-508 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                              - Transcript 1
                 3cns A   6 PAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLER------TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRP------ANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKL 509
                                    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      |  -   |   355       365       375       385       395       405       415    |    - |     435       445       455       465       475       485       495       505    
                                                                                                                                                                                                                                                                                                                                                                          342    349                                                                    420    427

Chain B from PDB  Type:PROTEIN  Length:487
 aligned with FMS1_YEAST | P50264 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             508 
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508 
           FMS1_YEAST     9 KKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLK-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cnsB01 B:9-91,B:196-289,B:445-509  [code=3.50.50.60, no name defined]             3cnsB02 B:92-195,B:290-444  [code=3.90.6     60.10, no name defined]                                    3cnsB01 B:9-91,B:196-289,B:445-509  [code=3.50.50.60, no name defined  ]                      3cnsB02 B:92-195,B:290-444  [code=3.90.660.10, no nam      e defined]                                                                                      3cnsB01 B:9-91,B:196-289,B:445-509                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhhh....eeee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhh.-----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh.......eee.hhhhhhhhhhh..hhh.ee....eeeeeee...eeeeee....eeee.eeee..hhhhhh.....--......eee...hhhhhhhh...eee..eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhhh.------.........eeeeehhhhhh..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee....-.........eeeeeee............eee......hhhhhhhhhhh....eee...........hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-508 (gaps) UniProt: 1-508 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                           - Transcript 1
                 3cns B   9 KKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFH-----SDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQP--NLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLER------TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRP-ENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKL 509
                                    18        28        38        48        58        68        78        88        98       108       118       128  |    138       148       158       168       178       188       198       208       218       228       238       248       258     | 268       278       288       298       308       318       328       338   |     -|      358       368       378       388       398       408       418 | |   428       438       448       458       468       478       488       498       508 
                                                                                                                                                    131   137                                                                                                                            264  |                                                                        342    349                                                                    420 |                                                                                       
                                                                                                                                                                                                                                                                                            267                                                                                                                                                        422

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 3CNS)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

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

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

Baker's yeast (Saccharomyces cerevisiae) (22)

1a	3cnsB01	B:9-91,B:196-289,B:445-509
1b	3cnsA01	A:6-91,A:196-289,A:445-509

Architecture: Alpha-Beta Complex (3881)

Topology: Polyamine Oxidase; Chain A, domain 2 (62)

Homologous Superfamily: [code=3.90.660.10, no name defined] (61)

Baker's yeast (Saccharomyces cerevisiae) (14)

2a	3cnsA02	A:92-195,A:290-444
2b	3cnsB02	B:92-195,B:290-444

(no "Pfam Domain" information available for 3CNS)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FMS1_YEAST | P50264)

molecular function
	GO:0052904	N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity	Catalysis of the reaction: H(2)O + N(1)-acetylspermidine + O(2) = 3-acetamidopropanal + H(2)O(2) + putrescine.
	GO:0052903	N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity	Catalysis of the reaction: H(2)O + N(1)-acetylspermine + O(2) = 3-acetamidopropanal + H(2)O(2) + spermidine.
	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:0046592	polyamine oxidase activity	Catalysis of the oxidative degradation or interconversion of polyamines.
	GO:0052902	spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity	Catalysis of the reaction: H(2)O + O(2) + spermidine = 3-aminopropanal + H(2)O(2) + putrescine.
	GO:0052901	spermine:oxygen oxidoreductase (spermidine-forming) activity	Catalysis of the reaction: H(2)O + O(2) + spermine = 3-aminopropanal + H(2)O(2) + spermidine.
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.
	GO:0015940	pantothenate biosynthetic process	The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
	GO:0046208	spermine catabolic process	The chemical reactions and pathways resulting in the breakdown of spermine, a polybasic amine found in human sperm, in ribosomes and in some viruses and involved in nucleic acid packaging.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:378 - Pro A:379	[ RasMol ]
		Ala B:378 - Pro B:379	[ RasMol ]
		Gln A:275 - Pro A:276	[ RasMol ]
		Gln B:275 - Pro B:276	[ RasMol ]

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1xpq	FMS1 IN COMPLEX WITH ITS NATIVE SUBSTRATE SPERMINE
1yy5	NATIVE FMS1
3cn8	FMS1 IN COMPLEX WITH SPERMIDINE
3cnd	FMS1 IN COMPLEX WITH N1-ACSPERMINE
3cnp	FMS1 IN COMPLEX WITH S-N1-ACMESPERMIDINE
3cnt	FMS1 IN COMPLEX WITH R-BZ-MESPERMIDINE

Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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