2O06 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   HUMAN SPERMIDINE SYNTHASE

Authors :   J. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   27 Nov 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Spermidine Synthase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wu, J. Min, Y. Ikeguchi, H. Zeng, A. Dong, P. Loppnau, A. E. Pegg, A. N. Plotnikov
Structure And Mechanism Of Spermidine Synthases.
Biochemistry V. 46 8331 2007
PubMed-ID: 17585781 | Reference-DOI: 10.1021/BI602498K
(for further references see the PDB file header)

Molecule 1 - SPERMIDINE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SRM, SPS1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PUTRESCINE AMINOPROPYLTRANSFERASE, SPDSY

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	MG	3	Ligand/Ion	MAGNESIUM ION
2	MTA	2	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
3	PUT	2	Ligand/Ion	1,4-DIAMINOBUTANE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN B:268	BINDING SITE FOR RESIDUE MG B 701
2	AC2	SOFTWARE	GLN A:268	BINDING SITE FOR RESIDUE MG A 702
3	AC3	SOFTWARE	HIS A:91 , ASP A:168 , ASP A:200 , GLY A:201	BINDING SITE FOR RESIDUE MG A 703
4	AC4	SOFTWARE	GLN A:49 , LEU A:65 , GLY A:101 , GLY A:103 , ASP A:104 , CYS A:123 , GLU A:124 , ILE A:125 , VAL A:129 , GLY A:154 , ASP A:155 , GLY A:156 , ASP A:173 , PRO A:180 , ALA A:181 , HOH A:931	BINDING SITE FOR RESIDUE MTA A 501
5	AC5	SOFTWARE	GLN B:49 , GLY B:101 , GLY B:102 , GLY B:103 , ASP B:104 , GLU B:124 , ILE B:125 , VAL B:129 , ASP B:155 , GLY B:156 , ASP B:173 , PRO B:180 , ALA B:181	BINDING SITE FOR RESIDUE MTA B 501
6	AC6	SOFTWARE	TRP A:28 , GLN A:70 , TYR A:79 , ASP A:173 , SER A:174 , ASP A:176 , TYR A:241 , PRO A:242 , HOH A:870 , HOH A:871	BINDING SITE FOR RESIDUE PUT A 601
7	AC7	SOFTWARE	GLN B:70 , TYR B:79 , ASP B:173 , SER B:174 , ASP B:176 , TYR B:241 , PRO B:242 , ILE B:246 , HOH B:787	BINDING SITE FOR RESIDUE PUT B 601

(no "SS Bond" information available for 2O06)

(no "Cis Peptide Bond" information available for 2O06)

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011807	L	149	V	SPEE_HUMAN	Polymorphism	1049932	A/B	L	149	V

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPEE_HUMAN	18-253	2	A:18-253 B:18-253
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPEE_HUMAN	97-110	2	A:97-110 B:97-110

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000376957	1a	ENSE00001836529	chr1:11120081-11119834	248	SPEE_HUMAN	1-56	56	2	A:6-56 B:14-56	51 43
1.2c	ENST00000376957	2c	ENSE00000743131	chr1:11119402-11119282	121	SPEE_HUMAN	56-96	41	2	A:56-96 B:56-96	41 41
1.3a	ENST00000376957	3a	ENSE00000743128	chr1:11118949-11118857	93	SPEE_HUMAN	97-127	31	2	A:97-127 B:97-127	31 31
1.4b	ENST00000376957	4b	ENSE00000743127	chr1:11116814-11116661	154	SPEE_HUMAN	128-179	52	2	A:128-179 B:128-179	52 52
1.5	ENST00000376957	5	ENSE00000743125	chr1:11116151-11116068	84	SPEE_HUMAN	179-207	29	2	A:179-207 B:179-207	29 29
1.6b	ENST00000376957	6b	ENSE00000743124	chr1:11115983-11115838	146	SPEE_HUMAN	207-255	49	2	A:207-255 B:207-255	49 49
1.7b	ENST00000376957	7b	ENSE00000743123	chr1:11115141-11115019	123	SPEE_HUMAN	256-296	41	2	A:256-296 B:256-296	41 41
1.7d	ENST00000376957	7d	ENSE00001847545	chr1:11114942-11114646	297	SPEE_HUMAN	297-302	6	2	A:297-302 B:297-302	6 6

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:297
 aligned with SPEE_HUMAN | P19623 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:297
                                    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       
           SPEE_HUMAN     6 DGPAASGPAAIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALNDVS 302
               SCOP domains d2o06a_ A: Spermidine synthase                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------2o06A02 A:75-302 Vaccinia Virus protein VP39                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee...hhhhhhhhhhhhhh......eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhhhhh.....hhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------PABS_2  PDB: A:18-253 UniProt: 18-253                                                                                                                                                                                                       ------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:6-56 UniProt: 1-56 [INCOMPLETE]  ----------------------------------------Exon 1.3a  PDB: A:97-127       Exon 1.4b  PDB: A:128-179 UniProt: 128-179          ---------------------------Exon 1.6b  PDB: A:207-255 UniProt: 207-255       Exon 1.7b  PDB: A:256-296                1.7d   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.2c  PDB: A:56-96 UniProt: 56-96   ----------------------------------------------------------------------------------Exon 1.5  PDB: A:179-207     ----------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2o06 A   6 DGPAASGPAAIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALNDVS 302
                                    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

Chain B from PDB  Type:PROTEIN  Length:289
 aligned with SPEE_HUMAN | P19623 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:289
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293         
           SPEE_HUMAN    14 AAIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALNDVS 302
               SCOP domains d2o06b_ B: Spermidine synthase                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------2o06B02 B:75-302 Vaccinia Virus protein VP39                                                                                                                                                                                         CATH domains
           Pfam domains (1) -----Spermine_synth-2o06B01 B:19-261                                                                                                                                                                                                                    ----------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Spermine_synth-2o06B02 B:19-261                                                                                                                                                                                                                    ----------------------------------------- Pfam domains (2)
         Sec.struct. author ..ee..eeee.......eeeeeeeeeeeeeee....eeeeeee....eeeee..eeeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhh...eeeeeeee...hhh.eeeeeeee..............hhhhhhhh.....hhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----PABS_2  PDB: B:18-253 UniProt: 18-253                                                                                                                                                                                                       ------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: B:14-56 UniProt: 1-56      ----------------------------------------Exon 1.3a  PDB: B:97-127       Exon 1.4b  PDB: B:128-179 UniProt: 128-179          ---------------------------Exon 1.6b  PDB: B:207-255 UniProt: 207-255       Exon 1.7b  PDB: B:256-296                1.7d   Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.2c  PDB: B:56-96 UniProt: 56-96   ----------------------------------------------------------------------------------Exon 1.5  PDB: B:179-207     ----------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2o06 B  14 AAIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNFQEPVQPLTQQQVAQMQLKYYNSDVHRAAFVLPEFARKALNDVS 302
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: Spermidine synthase (17)

Protein domain: Spermidine synthase (11)

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

1a	d2o06a_	A:
1b	d2o06b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Human (Homo sapiens) (49)

1a	2o06A02	A:75-302
1b	2o06B02	B:75-302

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Spermine_synth (12)

Homo sapiens (Human) (2)

1a	Spermine_synth-2o06B01	B:19-261
1b	Spermine_synth-2o06B02	B:19-261

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SPEE_HUMAN | P19623)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0004766	spermidine synthase activity	Catalysis of the reaction: S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine.
	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:0006596	polyamine biosynthetic process	The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
	GO:0006595	polyamine metabolic process	The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups.
	GO:0008295	spermidine biosynthetic process	The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2o06)

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	2o06
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UniProtKB/Swiss-Prot
	SPEE_HUMAN \| P19623	:	2o05 2o07 2o0l 3rw9

2o05	CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH 5-METHYLTHIOADENOSINE
2o07	CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH 5-METHYLTHIOADENOSINE AND SPERMIDINE
2o0l	CRYSTAL STRUCTURE OF HUMAN SPERMIDINE SYNTHASE IN COMPLEX WITH DECARBOXYLATED S-ADENOSYLMETHIONINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

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Exons (8, 16)

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