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(-) Description

Title :  CRYSTAL STRUCTURES OF FMS1 IN COMPLEX WITH ITS INHIBITORS
 
Authors :  Q. Huang, Q. Hao
Date :  29 Nov 07  (Deposition) - 01 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enzyme-Inhibitor Complex, Polyamine Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Huang, Q. Hao
Crystal Structures Of Fms1 In Complex With Its Inhibitors
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYAMINE OXIDASE FMS1
    ChainsA, B
    EC Number1.5.3.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneFMS1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymFMS1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
12972Ligand/IonDODECANE-1,12-DIAMINE
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE 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 , GLY A:62 , ALA A:63 , SER A:64 , TRP A:65 , HIS A:67 , VAL A:223 , THR A:252 , VAL A:253 , PRO A:254 , GLY A:270 , LEU A:294 , 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 , HOH A:1003 , HOH A:1016 , HOH A:1017 , HOH A:1032 , HOH A:1034 , HOH A:1036BINDING SITE FOR RESIDUE FAD A 801
2AC2SOFTWAREHIS A:67 , LEU A:173 , TRP A:174 , HIS A:175 , ASP A:186 , LEU A:294 , TYR A:450 , SER A:451BINDING SITE FOR RESIDUE 297 A 1001
3AC3SOFTWAREGLY B:15 , GLY B:17 , ILE B:18 , ALA B:19 , 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 , GLY B:270 , LEU B:294 , 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 , HOH B:1004 , HOH B:1014 , HOH B:1015 , HOH B:1021 , HOH B:1060BINDING SITE FOR RESIDUE FAD B 802
4AC4SOFTWAREHIS B:67 , LEU B:173 , TRP B:174 , LEU B:375 , SER B:451 , ALA B:486 , GLY B:487 , CYS B:488BINDING SITE FOR RESIDUE 297 B 1002

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:221 -A:238
2B:221 -B:238

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BI2)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR020W1YMR020W.1XIII:315376-3169021527FMS1_YEAST1-5085082A:5-508 (gaps)
B:8-508 (gaps)
504
501

(-) Sequences/Alignments

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:494
 aligned with FMS1_YEAST | P50264 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:506
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 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 3bi2A01 A:5-91,A:196-289,A:445-510  [code=3.50.50.60, no name defined]                 3bi2A02 A:92-195,A:290-444  [code=3.90.660.10, no name defined]                                         3bi2A01 A:5-91,A:196-289,A:445-510  [code=3.50.50.60, no name defined]                        3bi2A02 A:92-195,A:290-444  [code=3.90.660.10, no name      defined]                                                                                       3bi2A01 A:5-91,A:196-289,A:445-510                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhh....eeee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh.......eee..hhhhhhhhhh..hhh.ee....eeeeee.....eeeee....eeeeeeeee..hhhhhhhhhh.........eee...hhhhhhhh...eee..eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhhh..-----.........eeeeehhhhh...eeeeee..hhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....ee...-------....eeeeeee............eee.....hhhhhhhhhhh.....eee...........hhhhhhhhhhhhhhhhhhhhhh. 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
                 3bi2 A   5 SPAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLERE-----TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMR-------ANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKLE 510
                                    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:499
 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 3bi2B01 B:8-91,B:196-289,B:445-511  [code=3.50.50.60, no name defined]              3bi2B02 B:92-195,B:290-444  [code=3.90.660.10, no name defined]                                         3bi2B01 B:8-91,B:196-289,B:445-511  [code=3.50.50.60, no name defined]                        3bi2B02 B:92-195,B:290-444  [code=3.90.660.10, no name      defined]                                                                                       3bi2B01 B:8-91,B:196-289,B:445-511                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eeeee..........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......hhhhhh.......eee.hhhhhhhhhhhhhhhh.eee...eeeeeee...eeeeee....eeeeeeeee..hhhhhh.............eee...hhhhhhhh........eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhh...-----.........eeeeehhhhhh..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee..............eeeeeee.....................hhhhhhhhhh.....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
                 3bi2 B   8 KKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEMSKFAELEFHQHLGVSDCSFFQLVMKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSMLERE-----TSVTCWSQPLFFVNLSKSTGVASFMMLMQAPLTNHIESIREDKERLFSFFQPVLNKIMKCLDSEDVIDGMRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFPGDDPVDMVVAMSNGQDSRIRFAGEHTIMDGAGCAYGAWESGRREATRISDLLKLEH 511
                                    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       457       467       477       487       497       507    
                                                                                                                                                                                                                                                                                                                                                                         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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3BI2)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BI2)

(-) Gene Ontology  (9, 9)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FMS1_YEAST | P502641rsg 1xpq 1yy5 1z6l 3bi4 3bi5 3bnm 3bnu 3cn8 3cnd 3cnp 3cns 3cnt 4ech 4gdp

(-) Related Entries Specified in the PDB File

3bi4 3bi5