1RLZ - JenaLib

Title :   DEOXYHYPUSINE SYNTHASE HOLOENZYME IN ITS HIGH IONIC STRENGTH, LOW PH CRYSTAL FORM

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)

Method :   X-RAY DIFFRACTION

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (0, 0)

Exons (9, 9)

Asymmetric Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000210060	1	ENSE00000836318	chr19:12792682-12792374	309	DHYS_HUMAN	1-69	69	1	A:9-69	61
1.2c	ENST00000210060	2c	ENSE00000836317	chr19:12791139-12790975	165	DHYS_HUMAN	70-124	55	1	A:70-124 (gaps)	55
1.3	ENST00000210060	3	ENSE00001625611	chr19:12790736-12790615	122	DHYS_HUMAN	125-165	41	1	A:125-165	41
1.4	ENST00000210060	4	ENSE00001676585	chr19:12790533-12790437	97	DHYS_HUMAN	165-197	33	1	A:165-197	33
1.5	ENST00000210060	5	ENSE00001750488	chr19:12790357-12790271	87	DHYS_HUMAN	198-226	29	1	A:198-226	29
1.7	ENST00000210060	7	ENSE00001723881	chr19:12788210-12788105	106	DHYS_HUMAN	227-262	36	1	A:227-262	36
1.8	ENST00000210060	8	ENSE00001720398	chr19:12788025-12787922	104	DHYS_HUMAN	262-296	35	1	A:262-296	35
1.9a	ENST00000210060	9a	ENSE00001698134	chr19:12786956-12786831	126	DHYS_HUMAN	297-338	42	1	A:297-338	42
1.10	ENST00000210060	10	ENSE00001736077	chr19:12786747-12786537	211	DHYS_HUMAN	339-369	31	1	A:339-369	31

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 
           DHYS_HUMAN     9 APAGALAAVLKHSSTLPPESTQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLEPLSQDEDQHADLTQSRRPLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFMHEKNED 369
               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 .hhhhhhhhh................hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------------.....eeeeee.hhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhh.....ee.....hhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhh...ee......hhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh.....eeeeee............hhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhhhhhhhhh... 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)
                 1rlz A   9 APAGALAAVLKHSSTLPPESTQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLE-----------------PLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFMHEKNED 369
                                    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)
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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)

CATH Domains (1, 1)

Pfam Domains (1, 1)

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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