3CNT - JenaLib

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

Authors :   Q. Huang, Q. Hao

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

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Molecule 1 - FMS1
	Chains	:	B, A
	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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SP9	1	Ligand/Ion	N-{(1R)-3-[(4-AMINOBUTYL)AMINO]-1-METHYLPROPYL}BENZAMIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:15 , GLY A:17 , ILE A:18 , ALA A:19 , 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 , GLU A:222 , THR A:252 , PRO A:254 , GLY A:270 , LEU A:294 , TRP A:440 , 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 , LEU B:48 , GLY B:62 , ALA B:63 , SER B:64 , TRP B:65 , HIS B:67 , CYS B:221 , THR B:252 , 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 B:65 , HIS B:67 , LEU B:173 , TRP B:174 , PHE B:359 , LEU B:375 , TYR B:450 , ALA B:486 , CYS B:488	BINDING SITE FOR RESIDUE SP9 B 518

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

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

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

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

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:5-508 (gaps) B:8-508 (gaps)	504 501

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:497
 aligned with FMS1_YEAST | P50264 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:509
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 508     
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504   |     
           FMS1_YEAST     5 SPAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLK-----   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cntA01 A:5-91,A:196-289,A:445-513  [code=3.50.50.60, no name defined]                 3cntA02 A:92-195,A:290-444  [code=3.90.660.10, no name defined]                                         3cntA01 A:5-91,A:196-289,A:445-513  [code=3.50.50.60, no name defined]                        3cntA02 A:92-195,A:290-444  [code=3.90.660.10, no name      defined]                                                                                       3cntA01 A:5-91,A:196-289,A:445-513                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhh.....eee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhh.......eee..hhhhhhhhhh......ee....eeeeeee...eeeeee....eeeeeeeee..hhhhhhhhhh.........eee...hhhhhhhhhhheee..eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhhh..-----.........eeeeehhhhh...eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee...-------....eeeeeee............eee.....hhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-508 (gaps) UniProt: 1-508 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                               ----- Transcript 1
                 3cnt A   5 SPAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLERE-----TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMR-------ANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKLEHHH 513
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334        |-    |  354       364       374       384       394       404       414    |    -  |    434       444       454       464       474       484       494       504         
                                                                                                                                                                                                                                                                                                                                                                            343   349                                                                   419     427

Chain B from PDB  Type:PROTEIN  Length:495
 aligned with FMS1_YEAST | P50264 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              508   
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507|   
           FMS1_YEAST     8 KKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLEREDSQKHTSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLK---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3cntB01 B:8-91,B:196-289,B:445-511  [code=3.50.50.60, no name defined]              3cntB02 B:92-195,B:290-444  [code=3.90.660.    10, no name defined]                                     3cntB01 B:8-91,B:196-289,B:445-511  [code=3.50.50.60, no name defined]                        3cntB02 B:92-195,B:290-444  [code=3.90.660.10, no name      defined]                                                                                       3cntB01 B:8-91,B:196-289,B:445-511                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eeee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhhh...----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhh.......eee..hhhhhhhhhhhhhhhhh.....eeeeeee...eeeeee....eeeeeeeee..hhhhhhhhhh.........eee...hhhhhhhh........eeeeeee..........eeeee...hhhhhhhhhhh...hhhhhh....-----.........eeeeehhhhhh..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee..............eeeeeee......................hhhhhhhh......eee...........hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:8-508 (gaps) UniProt: 1-508 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                            --- Transcript 1
                 3cnt B   8 KKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHL----CSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLERE-----TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKLEH 511
                                    17        27        37        47        57        67        77        87        97       107       117       127      |  - |     147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337     |   - |     357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507    
                                                                                                                                                        134  139                                                                                                                                                                                                         343   349

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 3CNT)

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	3cntB01	B:8-91,B:196-289,B:445-511
1b	3cntA01	A:5-91,A:196-289,A:445-513

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	3cntA02	A:92-195,A:290-444
2b	3cntB02	B:92-195,B:290-444

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

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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	3cnt
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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
3cns	FMS1 IN COMPLEX WITH S-BZ-MESPERMIDINE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (1, 2)

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