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Title :   CRYSTAL STRUCTURE OF TRIAMINE/AGMATINE AMINOPROPYLTRANSFERASE (SPEE) FROM THERMUS THERMOPHILUS, COMPLEXED WITH MTA

Authors :   T. Ganbe, M. Ohnuma, T. Sato, N. Tanaka, T. Oshima, T. Kumasaka

Date :   14 Sep 10 (Deposition) - 13 Apr 11 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Spee, Spermine Synthase, Spermidine Synthase, Polyamine, Spermidine Biosynthesis, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Ohnuma, T. Ganbe, Y. Terui, M. Niitsu, T. Sato, N. Tanaka, M. Tamakoshi, K. Samejima, T. Kumasaka, T. Oshima
Crystal Structures And Enzymatic Properties Of A Triamine/Agmatine Aminopropyltransferase From Thermus Thermophilus
J. Mol. Biol. V. 408 971 2011
PubMed-ID: 21458463 | Reference-DOI: 10.1016/J.JMB.2011.03.025

Molecule 1 - SPERMIDINE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21C
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	POLYAMINE AMINOPROPYLTRANSFERASE, TRIAMINE/AGMATINE AMINOPROPYLTRANSFERASE, AGMATINE/SPERMIDINE AMINOPROPYLTRANSFERASE

		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	MTA	2	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MTA	4	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:33 , GLN A:54 , GLY A:85 , GLY A:86 , GLY A:87 , ASP A:108 , ILE A:109 , LEU A:113 , ASP A:140 , ALA A:141 , ASP A:158 , THR A:160 , LEU A:172	BINDING SITE FOR RESIDUE MTA A 315
2	AC2	SOFTWARE	GLN B:33 , GLY B:85 , GLY B:86 , GLY B:87 , VAL B:107 , ASP B:108 , ILE B:109 , LEU B:113 , ALA B:141 , ASP B:158 , LEU B:159 , LEU B:172	BINDING SITE FOR RESIDUE MTA B 315

(no "SS Bond" information available for 3ANX)

(no "Cis Peptide Bond" information available for 3ANX)

(no "SAP(SNP)/Variant" information available for 3ANX)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPEE_THET8	4-241	2	A:4-241 B:4-241
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPEE_THET8	81-94	2	A:81-94 B:81-94

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPEE_THET8	4-241	4	A:4-241 B:4-241
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPEE_THET8	81-94	4	A:81-94 B:81-94

(no "Exon" information available for 3ANX)

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:312
 aligned with SPEE_THET8 | Q5SK28 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
           SPEE_THET8     1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQAGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPY 312
               SCOP domains d3anxa_ A: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee..eeeeee.....eeee....eeeeee.....eeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhhheeeeeeeeeeeeee.....hhhhhhhhhhhhhh.eeeeeeeeehhhheeeeeeeee..........hhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhh.........eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---PABS_2  PDB: A:4-241 UniProt: 4-241                                                                                                                                                                                                           ----------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------PABS_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3anx A   1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQAGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPY 312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:313
 aligned with SPEE_THET8 | Q5SK28 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:313
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310   
           SPEE_THET8     1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQAGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPYK 313
               SCOP domains d3anxb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....eeeeeee.eeeeee......eeeeee...eeeeee..eeeeehhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhh......eeeee..hhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhheeeeeeeeeeeee......hhhhhhhhhhhh...eeeeeeee.hhhh.eeeeeeee........hhhhhhhhhhhh.......hhhhhhhh...hhhhhhhhhhh.........eee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PABS_2  PDB: B:4-241 UniProt: 4-241                                                                                                                                                                                                           ------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3anx B   1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQAGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPYK 313
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: automated matches (5)

Thermus thermophilus HB8 [TaxId: 300852] (1)

1a	d3anxa_	A:
1b	d3anxb_	B:

(no "CATH Domain" information available for 3ANX)

(no "Pfam Domain" information available for 3ANX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SPEE_THET8 | Q5SK28)

molecular function
	GO:0043919	agmatine aminopropyltransferase activity	Catalysis of the reaction: agmatine + S-adenosylmethioninamine = N1-aminopropylagmatine + 5'-methylthioadenosine.
	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:0004766	spermidine synthase activity	Catalysis of the reaction: S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine.
	GO:0010487	thermospermine synthase activity	Catalysis of the reaction: S-adenosyl-L-methioninamine + spermidine = S-methyl-5'-thioadenosine + thermospermine + H+.
	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:0008295	spermidine biosynthetic process	The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Biological Unit
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