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(-) Description

Authors :  T. C. Umland, E. C. Wolff, M. -H. Park, D. R. Davies
Date :  26 Nov 03  (Deposition) - 13 Jul 04  (Release) - 12 Nov 14  (Revision)
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Rossmann Fold, Nad Cofactor, Deoxyhypusine, Hypusine, Spermidine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  T. C. Umland, E. C. Wolff, M. -H. Park, D. R. Davies
A New Crystal Structure Of Deoxyhypusine Synthase Reveals The Configuration Of The Active Enzyme And Of An Enzyme-Nad-Inhibitor Ternary Complex
J. Biol. Chem. V. 279 28697 2004
PubMed-ID: 15100216  |  Reference-DOI: 10.1074/JBC.M404095200
(for further references see the PDB file header)

(-) Compounds

    EC Number2.5.1.46
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDHPS, DS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
1AC1SOFTWARETHR A:104 , SER A:105 , ASN A:106 , LEU A:107 , SER A:109 , THR A:131 , ALA A:132 , GLY A:133 , GLU A:137 , ASP A:238 , GLY A:282 , GLY A:283 , GLY A:284 , VAL A:285 , HIS A:288 , ILE A:306 , ASN A:307 , THR A:308 , ALA A:309 , ASP A:313 , SER A:315 , ASP A:316 , SER A:317 , ALA A:341 , ASP A:342 , ALA A:343 , HOH A:702 , HOH A:707BINDING SITE FOR RESIDUE NAD A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RLZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RLZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2cENST000002100602cENSE00000836317chr19:12791139-12790975165DHYS_HUMAN70-124551A:70-124 (gaps)55

(-) Sequences/Alignments

Asymmetric 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:344
 aligned with DHYS_HUMAN | P49366 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:361
                                    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 
               SCOP domains d1rlza_ A: Deoxyhypusine synthase, DHS                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1rlzA00 A:9-369 Deoxyhypusine Synthase                                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------DS-1rlzA01 A:42-356                                                                                                                                                                                                                                                                                                        ------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------D--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:9-69 UniProt: 1-69 [INCOMPLETE]             Exon 1.2c  PDB: A:70-124 (gaps) UniProt: 70-124        Exon 1.3  PDB: A:125-165 UniProt: 125-165--------------------------------Exon 1.5  PDB: A:198-226     Exon 1.7  PDB: A:227-262            ----------------------------------Exon 1.9a  PDB: A:297-338 UniProt: 297-338Exon 1.10  PDB: A:339-369       Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:165-197         ----------------------------------------------------------------Exon 1.8  PDB: A:262-296           ------------------------------------------------------------------------- Transcript 1 (2)
                                    18        28        38        48        58        68      |  -         -    |   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 
                                                                                             75                93                                                                                                                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
Clan: FAD_DHS (82)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (DHYS_HUMAN | P49366)
molecular function
    GO:0034038    deoxyhypusine synthase activity    Catalysis of the reaction: [eIF5A-precursor]-lysine + spermidine = [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine. Four sub-reactions have been identified,in which the intermediates remain tightly associated with the enzyme: spermidine + NAD+ = dehydrospermidine + NADH; dehydrospermidine + [enzyme]-lysine = N-(4-aminobutylidene)-[enzyme]-lysine + propane-1,3-diamine; N-(4-aminobutylidene)-[enzyme]-lysine + [eIF5A-precursor]-lysine = N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + [enzyme]-lysine; N-(4-aminobutylidene)-[eIF5A-precursor]-lysine + NADH + H+ = [eIF5A-precursor]-deoxyhypusine + NAD+.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0050983    obsolete deoxyhypusine biosynthetic process from spermidine    The chemical reactions resulting in the formation of deoxyhypusine from spermidine by the enzyme [eIF-5A]-deoxyhypusine synthase. The reaction occurs in four steps: 1. spermidine + NAD+ = dehydrospermidine + NADH + H+; 2. dehydrospermidine + [enzyme]-lysine = 1,3-diaminopropane + [enzyme]-lysine-N6=CH(CH2)3NH2; 3. [enzyme]-lysine-N6=CH(CH2)3NH2 = [eIF-5A]-lysine-N6=CH(CH2)3NH2; 4. [eIF-5A]-lysine-N6=CH(CH2)3NH2 + NADH + H+ = [eIF-5A]-deoxyhypusine + NAD+.
    GO:0008612    peptidyl-lysine modification to peptidyl-hypusine    The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.


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 Related Entries

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

        DHYS_HUMAN | P493661dhs 1roz 1rqd

(-) Related Entries Specified in the PDB File