1ROZ - JenaLib

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

Authors :   T. C. Umland, E. C. Wolff, M. -H. Park, D. R. Davies

Date :   02 Dec 03 (Deposition) - 13 Jul 04 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

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)

Molecule 1 - DEOXYHYPUSINE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.46
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DHPS, DS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DHS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:104 , SER A:105 , ASN A:106 , LEU A:107 , SER A:109 , THR A:131 , ALA A:132 , GLY A:133 , ASP A:238 , GLY A:282 , GLY A:283 , ASN A:307 , THR A:308 , ALA A:309 , ALA A:341 , ASP A:342 , ALA A:343 , HOH A:708 , HOH A:743 , HOH A:837 , HOH A:852 , GLY B:284 , VAL B:285 , HIS B:288 , ASP B:313 , SER B:315 , ASP B:316 , SER B:317 , HOH B:802	BINDING SITE FOR RESIDUE NAD A 701
2	AC2	SOFTWARE	GLY A:284 , VAL A:285 , HIS A:288 , ASP A:313 , SER A:315 , ASP A:316 , SER A:317 , HOH A:706 , 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:343 , HOH B:808 , HOH B:842 , HOH B:893 , HOH B:961	BINDING SITE FOR RESIDUE NAD B 801

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

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_043005	E	174	D	DHYS_HUMAN	Polymorphism	10425108	A/B	E	174	D

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

Biological Unit 1 (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_043005	E	174	D	DHYS_HUMAN	Polymorphism	10425108	A/B	E	174	D

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

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

Asymmetric Unit (9, 18)

	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	2	A:28-69 B:28-69	42 42
1.2c	ENST00000210060	2c	ENSE00000836317	chr19:12791139-12790975	165	DHYS_HUMAN	70-124	55	2	A:70-124 B:70-124 (gaps)	55 55
1.3	ENST00000210060	3	ENSE00001625611	chr19:12790736-12790615	122	DHYS_HUMAN	125-165	41	2	A:125-165 B:125-165	41 41
1.4	ENST00000210060	4	ENSE00001676585	chr19:12790533-12790437	97	DHYS_HUMAN	165-197	33	2	A:165-197 B:165-197	33 33
1.5	ENST00000210060	5	ENSE00001750488	chr19:12790357-12790271	87	DHYS_HUMAN	198-226	29	2	A:198-226 B:198-226	29 29
1.7	ENST00000210060	7	ENSE00001723881	chr19:12788210-12788105	106	DHYS_HUMAN	227-262	36	2	A:227-262 B:227-262	36 36
1.8	ENST00000210060	8	ENSE00001720398	chr19:12788025-12787922	104	DHYS_HUMAN	262-296	35	2	A:262-296 B:262-296	35 35
1.9a	ENST00000210060	9a	ENSE00001698134	chr19:12786956-12786831	126	DHYS_HUMAN	297-338	42	2	A:297-338 B:297-338	42 42
1.10	ENST00000210060	10	ENSE00001736077	chr19:12786747-12786537	211	DHYS_HUMAN	339-369	31	2	A:339-363 B:339-363	25 25

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:336
 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 d1roza_ A: Deoxyhypusine synthase, DHS                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1rozA00 A:28-363 Deoxyhypusine Synthase                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...........eeeeeehhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhh.....ee.....hhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhh...ee......hhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeeee............hhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhhhhhh 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:339-363 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:165-197         ----------------------------------------------------------------Exon 1.8  PDB: A:262-296           ------------------------------------------------------------------- Transcript 1 (2)
                 1roz A  28 STQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLEPLSQDEDQHADLTQSRRPLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFM 363
                                    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 d1rozb_ B: Deoxyhypusine synthase, DHS                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1rozB00 B:28-363 Deoxyhypusine Synthase                                                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) --------------DS-1rozB01 B:42-356                                                                                                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) --------------DS-1rozB02 B:42-356                                                                                                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author .......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------------.....eeeeeehhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhh.....ee.....hhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhh...ee......hhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeee...hhhhh.....hhhhhhhhh........eee..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)
                 1roz 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: DHS-like NAD/FAD-binding domain (176)

Superfamily: DHS-like NAD/FAD-binding domain (176)

Family: Deoxyhypusine synthase, DHS (4)

Protein domain: Deoxyhypusine synthase, DHS (4)

Human (Homo sapiens) [TaxId: 9606] (4)

1a	d1roza_	A:
1b	d1rozb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Deoxyhypusine Synthase (4)

Homologous Superfamily: Deoxyhypusine Synthase (4)

Human (Homo sapiens) (4)

1a	1rozA00	A:28-363
1b	1rozB00	B:28-363

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_DHS (82)

Family: DS (3)

Homo sapiens (Human) (3)

1a	DS-1rozB01	B:42-356
1b	DS-1rozB02	B:42-356

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.

Asymmetric Unit
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UniProtKB/Swiss-Prot
	DHYS_HUMAN \| P49366	:	1dhs 1rlz 1rqd

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

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

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Exons (9, 18)

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