1Z6L - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FMS1 IN COMPLEX WITH ITS SUBSTRATE

Authors :   Q. Huang, Q. Liu, Q. Hao

Date :   22 Mar 05 (Deposition) - 27 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Fms1, Bis(Hexamethylene)Triamine, Crystal Structure, Polyamine Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Q. Huang, Q. Liu, Q. Hao
Crystal Structure Of Fms1 In Complex With Its Substrate
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - POLYAMINE OXIDASE FMS1
	Chains	:	A, B
	EC Number	:	1.5.3.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	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	DRE	2	Ligand/Ion	N-(6-AMINOHEXYL)HEXANE-1,6-DIAMINE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

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:46 , ARG A:47 , LEU A:48 , GLY A:62 , ALA A:63 , SER A:64 , TRP A:65 , HIS A:67 , VAL A:223 , THR A:252 , PRO A:254 , GLY A:270 , 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 , DRE A:804 , HOH A:807 , HOH A:810 , HOH A:819 , HOH A:821 , HOH A:833	BINDING SITE FOR RESIDUE FAD A 803
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 , VAL B:223 , THR B:252 , VAL B:253 , 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 , DRE B:601 , HOH B:835	BINDING SITE FOR RESIDUE FAD B 804
3	AC3	SOFTWARE	HIS A:67 , TRP A:174 , ASP A:186 , PHE A:189 , TYR A:450 , SER A:451 , ALA A:486 , CYS A:488 , FAD A:803	BINDING SITE FOR RESIDUE DRE A 804
4	AC4	SOFTWARE	HIS B:67 , LEU B:173 , TRP B:174 , HIS B:175 , ASP B:186 , PHE B:189 , LEU B:375 , TYR B:450 , CYS B:453 , GLY B:487 , FAD B:804	BINDING SITE FOR RESIDUE DRE B 601

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 1Z6L)

(no "PROSITE Motif" information available for 1Z6L)

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:8-508 (gaps)	503 501

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:488
 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 1z6lA01 A:6-91,A:196-289,A:445-509  [code=3.50.50.60, no name defined]                1z6lA02 A:92-195,A:290-444  [code=3.90.660.10, no name defined]                                         1z6lA01 A:6-91,A:196-289,A:445-509  [code=3.50.50.60, no name defined]                        1z6lA02 A:92-195,A:290-444  [code=3.90.660.10, no nam      e defined]                                                                                      1z6lA01 A:6    -91,A:196-289,A:445-509                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhh....eeee...........eeeehhheeee....ee.....hhhhhhhhhhhhh.....ee......eeee...ee.......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh.......eee..hhhhhhhhhhhhhhh.ee....eeeeeee...eeeeee....eeeeeeeee..hhhhhhhhhh.........eee...hhhhhhhhh..eee..eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhhh.------.........eeeeehhhhhh..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee....------....eeeeeee............eee...----hhhhhhhhh.....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
                 1z6l A   6 PAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLER------TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRP------ANKPVLRNIIVSNWTRDPYSRGAYSACFP----VDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKL 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                         455  460

Chain B from PDB  Type:PROTEIN  Length:484
 aligned with FMS1_YEAST | P50264 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              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 1z6lB01 B:8-91,B:196-289,B:445-509  [code=3.50.50.60, no name defined]              1z6lB02 B:92-195,B:290-444  [code=3.90.6     60.10, no name defined]                                    1z6lB01 B:8-91,B:196-289,B:445-509  [code=3.50.50.60, no name defined  ]                      1z6lB02 B:92-195,B:290-444  [code=3.90.660.10, no nam      e defined]                                                                                      1z6lB01 B:8    -91,B:196-289,B:445-509                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eeee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhh.-----...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhh.......eee.hhhhhhhhhhh......ee....eeeeeee...eeeeee....eeeeeeeee..hhhhhh.....--......eee...hhhhhhhhhhheee..eeeeeee..........eeeee...hhhhhhhhh.....hhhhhhhh.------...hhhhh.eeeeehhhhhh..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee....-.........eeeeeee............eee...----.hhhhhhhhh....eee...........hhhhhhhhhhhhhhhhhhhhhh 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
                 1z6l B   8 KKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFH-----SDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQP--NLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLER------TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRP-ENIANANKPVLRNIIVSNWTRDPYSRGAYSACFP----VDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKL 509
                                    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    |    - |     357       367       377       387       397       407       417  | |  427       437       447       | -  |    467       477       487       497       507  
                                                                                                                                                     131   137                                                                                                                            264  |                                                                        342    349                                                                    420 |                              455  460                                                 
                                                                                                                                                                                                                                                                                             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 1Z6L)

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	1z6lB01	B:8-91,B:196-289,B:445-509
1b	1z6lA01	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	1z6lA02	A:92-195,A:290-444
2b	1z6lB02	B:92-195,B:290-444

(no "Pfam Domain" information available for 1Z6L)

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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	1z6l
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1rsg	SE-MET LABLED FMS1
1xpq	FMS1-SPERMINE COMPLEX
1yy5	NATIVE FMS1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

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CATH Domains (2, 4)

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