1UIR - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF POLYAMINE AMINOPROPYLTRANSFEASE FROM THERMUS THERMOPHILUS

Authors :   T. Ganbe, M. Ohnuma, T. Sato, T. Kumasaka, T. Oshima, N. Tanaka, Riken S Genomics/Proteomics Initiative (Rsgi)

Date :   18 Jul 03 (Deposition) - 05 Aug 03 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Spermidien Synthase, Spermine Synthase, Polyamine, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (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 - POLYAMINE AMINOPROPYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.5.1.16, 2.5.1.22
	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	:	274

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1UIR)

(no "Site" information available for 1UIR)

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

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

(no "SAP(SNP)/Variant" information available for 1UIR)

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

Biological Unit 2 (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

(no "Exon" information available for 1UIR)

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:309
 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 d1uira_ A: Spermidine synthase                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --1uirA01 A:3-54  [code=2.30.140.10, no name defined] -1uirA02 A:56-311 Vaccinia Virus protein VP39                                                                                                                                                                                                                    - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhhhheeeeeeeeeeeeee..---hhhhhhhhhhhh...eeeeeeee.hhhh.eeeeeeee..........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
                 1uir A   1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQTGMILL---RVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPY 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  
                                                                                                                                                                                                                                 200 204

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 d1uirb_ B: Spermidine synthase                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --1uirB01 B:3-54  [code=2.30.140.10, no name defined] -1uirB02 B:56-311 Vaccinia Virus protein VP39                                                                                                                                                                                                                    -- CATH domains
           Pfam domains (1) ----Spermine_synth-1uirB01 B:5-248                                                                                                                                                                                                                      ----------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----Spermine_synth-1uirB02 B:5-248                                                                                                                                                                                                                      ----------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeee....eeeeee..eeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhhh.eeeeeeeeeeeee......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
                 1uir B   1 MDYGMYFFEHVTPYETLVRRMERVIASGKTPFQDYFLFESKGFGKVLILDKDVQSTERDEYIYHETLVHPAMLTHPEPKRVLIVGGGEGATLREVLKHPTVEKAVMVDIDGELVEVAKRHMPEWHQGAFDDPRAVLVIDDARAYLERTEERYDVVIIDLTDPVGEDNPARLLYTVEFYRLVKAHLNPGGVMGMQTGMILLTHHRVHPVVHRTVREAFRYVRSYKNHIPGFFLNFGFLLASDAFDPAAFSEGVIEARIRERNLALRHLTAPYLEAMFVLPKDLLEALEKETMVSTDQNPFYVTPEGEARQAPYK 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(

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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: Spermidine synthase (11)

Thermus thermophilus [TaxId: 274] (1)

1a	d1uira_	A:
1b	d1uirb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Thermus thermophilus. Organism_taxid: 274. (1)

1a	1uirA02	A:56-311
1b	1uirB02	B:56-311

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Spermidine Synthase; Chain: A, domain 2 (12)

Homologous Superfamily: [code=2.30.140.10, no name defined] (9)

Thermus thermophilus. Organism_taxid: 274. (1)

2a	1uirA01	A:3-54
2b	1uirB01	B:3-54

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Spermine_synth (12)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (1)

1a	Spermine_synth-1uirB01	B:5-248
1b	Spermine_synth-1uirB02	B:5-248

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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1inl
1iy9
1jq3
1mjf	RELATED ID: TTK003000339.1 RELATED DB: TARGETDB

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