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(-) Description

Title :  CRYSTAL STRUCTURE OF THE POLYAMINE OXIDASE FMS1 FROM YEAST
 
Authors :  Q. Huang, Q. Liu, Q. Hao
Date :  09 Dec 03  (Deposition) - 15 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fad Binding Motif, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Huang, Q. Liu, Q. Hao
Crystal Structures Of Fms1 And Its Complex With Spermine Reveal Substrate Specificity.
J. Mol. Biol. V. 348 951 2005
PubMed-ID: 15843025  |  Reference-DOI: 10.1016/J.JMB.2005.03.008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FMS1 PROTEIN
    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, YMR020W, YM9711.09
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric/Biological Unit (2, 24)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY 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 , VAL A:223 , THR A:252 , VAL A:253 , PRO A:254 , GLY A:270 , LEU A:294 , LYS A:296 , TRP A:440 , TYR A:445 , GLY A:478 , GLU A:479 , GLY A:487 , CYS A:488 , ALA A:489 , ALA A:492 , HOH A:1802 , HOH A:1805 , HOH A:1808 , HOH A:1810 , HOH A:1815 , HOH A:1836 , HOH A:2168BINDING SITE FOR RESIDUE FAD A 1801
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:45 , 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 , GLY B:478 , GLU B:479 , GLY B:487 , CYS B:488 , ALA B:489 , ALA B:492 , HOH B:1808 , HOH B:1821 , HOH B:1822 , HOH B:1838 , HOH B:1868 , HOH B:1905 , HOH B:2032BINDING SITE FOR RESIDUE FAD B 1802

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:221 -A:238
2A:453 -A:488
3B:221 -B:238
4B:453 -B:488

(-) 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 1RSG)

(-) PROSITE Motifs  (0, 0)

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

(-) 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:8-508 (gaps)
503
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:481
 aligned with FMS1_YEAST | P50264 from UniProtKB/Swiss-Prot  Length:508

    Alignment length:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                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 1rsgA01 A:6-91,A:196-289,A:445-513  [code=3.50.50.60, no name defined]                1rsgA02 A:92-195,A:290-444  [code=3.90.       660.10, no name defined]                                  1rsgA01 A:6-91,A:196-289,A:445-513  [code=3.50.50.60, no name defined]                        1rsgA02 A:92-195,A:290-444  [code=3.90.660.10, no n         ame defined]                                                                                   1rsgA01 A:6    -91,A:196-289,A:445-513                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhh....eeee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhh-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhh.......eee.hhhhhhhhhhhhhhhh.ee....eeeeee.....eeeee....eeeeeeeee..hhhhhhhhhh.........eee...hhhhhhhh........eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhh---------........eeeeehhhhh...eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee...-------....eeeeeee..................----hhhhhhhhhh....eee...........hhhhhhhhhhhhhhhhhhhhhhhhh. 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
                 1rsg A   6 PAKKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEmSKFAELEF-------DCSFFQLVmKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSmL---------SVTCWSQPLFFVNLSKSTGVASFmmLmQAPLTNHIESIREDKERLFSFFQPVLNKImKCLDSEDVIDGmR-------ANKPVLRNIIVSNWTRDPYSRGAYSACFP----VDmVVAmSNGQDSRIRFAGEHTImDGAGCAYGAWESGRREATRISDLLKLEHHH 513
                                    15        25        35        45        55        65        75        85        95       105       115      |125    |    -  |    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        
                                                                                                                                              122-MSE 130     138     146-MSE                                                                                                                                                                                          339-MSE    350                    373-MSE                          406-MSE     418-MSE  427                         455  460 |   |              483-MSE                          
                                                                                                                                                                                                                                                                                                                                                                        340                               374-MSE                                      419                                        462-MSE                                               
                                                                                                                                                                                                                                                                                                                                                                                                            376-MSE                                                                                   466-MSE                                           

Chain B from PDB  Type:PROTEIN  Length:491
 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 1rsgB01 B:8-47,B:200-290,B:455-511      1rsgB02 B:48-199,B:291-454  [code=3.90.660.10, no name defined]                                                                                         1rsgB01 B:8-47,B:200-290,B:455-511  [code=3.50.50.60, no name defined]                     1rsgB02 B:48-199,B:291-454  [code=3.90.660.10, no nam     e defined]                                                                                                1    rsgB01 B:8-47,B:200-290,B:455-511                    CATH domains
           Pfam domains (1) ----------Amino_oxidase-1rsgB01 B:18-504                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------- Pfam domains (1)
           Pfam domains (2) ----------Amino_oxidase-1rsgB02 B:18-504                                                                                                                                                                                                                                                                                                                                                                                                                                                                         ------- Pfam domains (2)
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eeee...........eee.hhh.eee....ee.....hhhhhhhhhhhhhhh...ee......eeee...ee.......hhhhhhhhhhhhhhhhh....----.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......hhhhhh.......eee.hhhhhhhhhhhhhhhh.ee....eeeeee.....eeeee....eeeeeeeee..hhhhhhhh...........eee...hhhhhhhh........eeeeeee..........eeee....hhhhhhhhhhh.hhhhhhhhh...-----.........eeeeehhhhhh..eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....ee......hhhhh...eeeeeee..................----hhhhhhhhhh....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
                 1rsg B   8 KKKVIIIGAGIAGLKAASTLHQNGIQDCLVLEARDRVGGRLQTVTGYQGRKYDIGASWHHDTLTNPLFLEEAQLSLNDGRTRFVFDDDNFIYIDEERGRVDHDKELLLEIVDNEmSKFAELEFHQHL----CSFFQLVmKYLLQRRQFLTNDQIRYLPQLCRYLELWHGLDWKLLSAKDTYFGHQGRNAFALNYDSVVQRIAQSFPQNWLKLSCEVKSITREPSKNVTVNCEDGTVYNADYVIITVPQSVLNLSVQPEKNLRGRIEFQPPLKPVIQDAFDKIHFGALGKVIFEFEECCWSNESSKIVTLANSTNEFVEIVRNAENLDELDSmLERE-----TSVTCWSQPLFFVNLSKSTGVASFmmLmQAPLTNHIESIREDKERLFSFFQPVLNKImKCLDSEDVIDGmRPIENIANANKPVLRNIIVSNWTRDPYSRGAYSACFP----VDmVVAmSNGQDSRIRFAGEHTImDGAGCAYGAWESGRREATRISDLLKLEH 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       | -  | |  467       477     | 487       497       507    
                                                                                                                                            122-MSE     134  139      |                                                                                                                                                                                              339-MSE   349                     373-MSE                          406-MSE     418-MSE                              455  460 |   |              483-MSE                        
                                                                                                                                                                    146-MSE                                                                                                                                                                                                                             374-MSE                                                                                 462-MSE                                             
                                                                                                                                                                                                                                                                                                                                                                                                          376-MSE                                                                                   466-MSE                                         

   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 1RSG)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) 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 | P502641xpq 1yy5 1z6l 3bi2 3bi4 3bi5 3bnm 3bnu 3cn8 3cnd 3cnp 3cns 3cnt 4ech 4gdp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RSG)