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(-) Description

Title :  DEOXYHYPUSINE SYNTHASE HOLOENZYME IN ITS LOW IONIC STRENGTH, HIGH PH CRYSTAL FORM WITH THE INHIBITOR GC7 BOUND IN THE ACTIVE SITE
 
Authors :  T. C. Umland, E. C. Wolff, M. -H. Park, D. R. Davies
Date :  04 Dec 03  (Deposition) - 13 Jul 04  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rossmann Fold, Nad Cofactor, Deoxyhypusine, Hypusine, Spermidine, Gc7, 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

Molecule 1 - DEOXYHYPUSINE SYNTHASE
    ChainsA, B
    EC Number2.5.1.46
    EngineeredYES
    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
    SynonymDHS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GC72Ligand/Ion1-GUANIDINIUM-7-AMINOHEPTANE
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GC74Ligand/Ion1-GUANIDINIUM-7-AMINOHEPTANE
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:104 , SER A:105 , ASN A:106 , SER A:109 , THR A:131 , ALA A:132 , GLY A:133 , GLU A:137 , ASP A:238 , GLY A:282 , GLY A:283 , ILE A:306 , ASN A:307 , THR A:308 , ALA A:309 , ALA A:341 , ASP A:342 , ALA A:343 , GLY B:284 , HIS B:288 , ASP B:313 , SER B:315 , ASP B:316 , SER B:317 , NAD B:370 , GC7 B:371BINDING SITE FOR RESIDUE NAD A 370
2AC2SOFTWAREGLY A:284 , VAL A:285 , HIS A:288 , ASP A:313 , SER A:315 , ASP A:316 , SER A:317 , NAD A:370 , GC7 A:371 , THR B:104 , SER B:105 , ASN B:106 , LEU B:107 , SER B:109 , THR B:131 , ALA B:132 , GLY B:133 , GLU B:137 , ASP B:238 , GLY B:282 , GLY B:283 , ASN B:307 , THR B:308 , ALA B:309 , ALA B:341 , ASP B:342 , ALA B:343BINDING SITE FOR RESIDUE NAD B 370
3AC3SOFTWAREHIS A:288 , ASN A:292 , LEU A:295 , GLY A:314 , SER A:315 , ASP A:316 , GLU A:323 , TRP A:327 , LYS A:329 , ASP B:243 , NAD B:370BINDING SITE FOR RESIDUE GC7 A 371
4AC4SOFTWAREILE A:166 , GLY A:167 , ASP A:243 , NAD A:370 , HIS B:288 , ASN B:292 , GLY B:314 , SER B:315 , ASP B:316 , GLU B:323 , TRP B:327 , LYS B:329BINDING SITE FOR RESIDUE GC7 B 371

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043005E174DDHYS_HUMANPolymorphism10425108A/BE174D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043005E174DDHYS_HUMANPolymorphism10425108A/BE174D

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (9, 18)

Asymmetric Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002100601ENSE00000836318chr19:12792682-12792374309DHYS_HUMAN1-69692A:28-69
B:28-69
42
42
1.2cENST000002100602cENSE00000836317chr19:12791139-12790975165DHYS_HUMAN70-124552A:70-124
B:70-124 (gaps)
55
55
1.3ENST000002100603ENSE00001625611chr19:12790736-12790615122DHYS_HUMAN125-165412A:125-165
B:125-165
41
41
1.4ENST000002100604ENSE00001676585chr19:12790533-1279043797DHYS_HUMAN165-197332A:165-197
B:165-197
33
33
1.5ENST000002100605ENSE00001750488chr19:12790357-1279027187DHYS_HUMAN198-226292A:198-226
B:198-226
29
29
1.7ENST000002100607ENSE00001723881chr19:12788210-12788105106DHYS_HUMAN227-262362A:227-262
B:227-262
36
36
1.8ENST000002100608ENSE00001720398chr19:12788025-12787922104DHYS_HUMAN262-296352A:262-296
B:262-296
35
35
1.9aENST000002100609aENSE00001698134chr19:12786956-12786831126DHYS_HUMAN297-338422A:297-338
B:297-338
42
42
1.10ENST0000021006010ENSE00001736077chr19:12786747-12786537211DHYS_HUMAN339-369312A:339-364
B:339-363
26
25

(-) 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:337
 aligned with DHYS_HUMAN | P49366 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:337
                                    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       
           DHYS_HUMAN    28 STQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLEPLSQDEDQHADLTQSRRPLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFMH 364
               SCOP domains d1rqda_ A: Deoxyhypusine synthase, DHS                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1rqdA00 A:28-364 Deoxyhypusine Synthase                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...........eeeeee.hhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhh.....ee.....hhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhh...ee......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeeee............hhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:28-69 UniProt: 1-69      Exon 1.2c  PDB: A:70-124 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:339-364  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:165-197         ----------------------------------------------------------------Exon 1.8  PDB: A:262-296           -------------------------------------------------------------------- Transcript 1 (2)
                 1rqd A  28 STQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLEPLSQDEDQHADLTQSRRPLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFMH 364
                                    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       

Chain B from PDB  Type:PROTEIN  Length:321
 aligned with DHYS_HUMAN | P49366 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:336
                                    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      
           DHYS_HUMAN    28 STQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLEPLSQDEDQHADLTQSRRPLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFM 363
               SCOP domains d1rqdb_ B: Deoxyhypusine synthase, DHS                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1rqdB00 B:28-363 Deoxyhypusine Synthase                                                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) --------------DS-1rqdB01 B:42-356                                                                                                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) --------------DS-1rqdB02 B:42-356                                                                                                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author .......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---------------.....eeeeee.hhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhh.....ee.....hhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhh...ee......hhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeeee............hhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------D--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:28-69 UniProt: 1-69      Exon 1.2c  PDB: B:70-124 (gaps) UniProt: 70-124        Exon 1.3  PDB: B:125-165 UniProt: 125-165--------------------------------Exon 1.5  PDB: B:198-226     Exon 1.7  PDB: B:227-262            ----------------------------------Exon 1.9a  PDB: B:297-338 UniProt: 297-338Exon 1.10  PDB: B:339-363 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: B:165-197         ----------------------------------------------------------------Exon 1.8  PDB: B:262-296           ------------------------------------------------------------------- Transcript 1 (2)
                 1rqd B  28 STQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLEPL---------------PLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFM 363
                                    37        47        57        67        77         -     |  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      
                                                                            77              93                                                                                                                                                                                                                                                                              

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: FAD_DHS (82)
(-)
Family: DS (3)
1aDS-1rqdB01B:42-356
1bDS-1rqdB02B:42-356

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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)

UniProtKB/Swiss-Prot
        DHYS_HUMAN | P493661dhs 1rlz 1roz

(-) Related Entries Specified in the PDB File

1dhs DEOXYHYPUSINE SYNTHASE HOLOENZYME IN ITS HIGH IONIC STRENGTH, LOW PH CRYSTAL FORM; GROWN FROM A DIFFERENT DHS PREPARATION THAN THE CURRENT STUDY
1rlz DEOXYHYPUSINE SYNTHASE HOLOENZYME IN ITS HIGH IONIC STRENGTH, LOW PH CRYSTAL FORM; GROWN FROM THE SAME DHS PREPARATION AS THE CURRENT STUDY
1roz DEOXYHYPUSINE SYNTHASE HOLOENZYME IN ITS LOW IONIC STRENGTH, HIGH PH CRYSTAL FORM