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(-) Description

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)

(-) Compounds

Molecule 1 - FMS1
    ChainsA, B
    EC Number1.5.3.11
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneFMS1
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymFENPROPIMORPH RESISTANCE MULTICOPY SUPPRESSOR 1

 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
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2SP82Ligand/IonN-{(1S)-3-[(4-AMINOBUTYL)AMINO]-1-METHYLPROPYL}BENZAMIDE

(-) 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: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:492BINDING SITE FOR RESIDUE FAD A 517
2AC2SOFTWAREGLY 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:492BINDING SITE FOR RESIDUE FAD B 517
3AC3SOFTWARETRP 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:450BINDING SITE FOR RESIDUE SP8 A 518
4AC4SOFTWARETRP B:65 , HIS B:67 , LEU B:173 , TRP B:174 , LEU B:294 , LEU B:375 , TYR B:450 , GLY B:487BINDING SITE FOR RESIDUE SP8 B 518

(-) 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 3CNS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR020W1YMR020W.1XIII:315376-3169021527FMS1_YEAST1-5085082A:6-508 (gaps)
B:9-508 (gaps)
503
500

(-) 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: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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3bi2 3bi4 3bi5 3bnm 3bnu 3cn8 3cnd 3cnp 3cnt 4ech 4gdp

(-) Related Entries Specified in the PDB File

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