3C6M - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN SPERMINE SYNTHASE IN COMPLEX WITH SPERMINE AND 5-METHYLTHIOADENOSINE

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

Date :   04 Feb 08 (Deposition) - 19 Feb 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Spermidine Aminopropyltransferase, Spmsy, Structural Genomics, Structural Genomics Consortium, Sgc, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wu, J. Min, H. Zeng, D. E. Mccloskey, Y. Ikeguchi, P. Loppnau, A. J. Michael, A. E. Pegg, A. N. Plotnikov
Crystal Structure Of Human Spermine Synthase: Implications Of Substrate Binding And Catalytic Mechanism.
J. Biol. Chem. V. 283 16135 2008
PubMed-ID: 18367445 | Reference-DOI: 10.1074/JBC.M710323200
(for further references see the PDB file header)

Molecule 1 - SPERMINE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	2.5.1.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-LIC
	Expression System Strain	:	BL21(DE3) CODON PLUS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SMS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SPERMIDINE AMINOPROPYLTRANSFERASE, SPMSY

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

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

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	MTA	2	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SPM	2	Ligand/Ion	SPERMINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	MTA	2	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SPM	2	Ligand/Ion	SPERMINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:124 , PRO A:125 , TYR A:134 , ASP A:167 , VAL A:168 , ASN A:169 , TYR A:177 , ASP A:201 , ASP A:276 , LEU A:277 , TYR A:351 , GLU A:353 , TRP A:355 , HOH A:571 , HOH A:576	BINDING SITE FOR RESIDUE SPM A 501
2	AC2	SOFTWARE	ASP B:167 , VAL B:168 , ASN B:169 , TYR B:177 , ASP B:201 , ASP B:276 , LEU B:277 , GLN B:315 , TYR B:351 , GLU B:353 , TRP B:355 , MTA B:401 , HOH B:524	BINDING SITE FOR RESIDUE SPM B 501
3	AC3	SOFTWARE	ASP C:167 , VAL C:168 , ASN C:169 , TYR C:177 , ASP C:201 , ASP C:276 , LEU C:277 , GLN C:315 , TYR C:351 , GLU C:353 , TRP C:355 , MTA C:401 , HOH C:527 , HOH C:536 , HOH C:563	BINDING SITE FOR RESIDUE SPM C 501
4	AC4	SOFTWARE	TRP D:124 , THR D:126 , TYR D:134 , ASP D:167 , VAL D:168 , ASN D:169 , TYR D:177 , ASP D:201 , ASP D:276 , GLN D:315 , TYR D:351 , GLU D:353 , TRP D:355	BINDING SITE FOR RESIDUE SPM D 501
5	AC5	SOFTWARE	GLN A:148 , LEU A:162 , LEU A:164 , ASN A:169 , GLY A:198 , GLY A:199 , GLY A:200 , ASP A:201 , VAL A:219 , GLU A:220 , ILE A:221 , ASP A:222 , VAL A:225 , ASP A:255 , CYS A:256 , ASP A:276 , LEU A:277 , THR A:278 , ILE A:282	BINDING SITE FOR RESIDUE MTA A 401
6	AC6	SOFTWARE	GLN B:148 , LEU B:162 , LEU B:164 , ASN B:169 , GLY B:198 , GLY B:199 , ASP B:201 , VAL B:219 , GLU B:220 , ILE B:221 , ASP B:222 , VAL B:225 , ASP B:255 , CYS B:256 , ASP B:276 , LEU B:277 , THR B:278 , ILE B:282 , SPM B:501	BINDING SITE FOR RESIDUE MTA B 401
7	AC7	SOFTWARE	GLN C:148 , LEU C:162 , LEU C:164 , ASN C:169 , GLY C:198 , GLY C:199 , GLY C:200 , ASP C:201 , VAL C:219 , GLU C:220 , ILE C:221 , VAL C:225 , ASP C:255 , CYS C:256 , ASP C:276 , LEU C:277 , THR C:278 , ILE C:282 , SPM C:501	BINDING SITE FOR RESIDUE MTA C 401
8	AC8	SOFTWARE	GLN D:148 , LEU D:164 , ASN D:169 , GLY D:198 , GLY D:199 , GLY D:200 , ASP D:201 , VAL D:219 , GLU D:220 , ILE D:221 , VAL D:225 , ASP D:255 , CYS D:256 , ASP D:276 , LEU D:277 , THR D:278 , ILE D:282	BINDING SITE FOR RESIDUE MTA D 401

(no "SS Bond" information available for 3C6M)

Asymmetric Unit

No.	Residues
1	Gln A:74	-	Ser A:75

Asymmetric Unit (6, 17)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_076449	G	56	S	SPSY_HUMAN	Disease (MRXSSR)	121434610	A/B	G	56	S
2	UniProt	VAR_072748	F	58	L	SPSY_HUMAN	Disease (MRXSSR)	397515549	A/B	F	58	L
3	UniProt	VAR_071048	N	60	S	SPSY_HUMAN	Polymorphism	---	A/B	N	60	S
4	UniProt	VAR_076450	G	67	E	SPSY_HUMAN	Disease (MRXSSR)	397515550	A/B/D	G	67	E
5	UniProt	VAR_076451	V	132	G	SPSY_HUMAN	Disease (MRXSSR)	267607076	A/B/C/D	V	132	G
6	UniProt	VAR_076452	Y	328	C	SPSY_HUMAN	Disease (MRXSSR)	397515553	A/B/C/D	Y	328	C

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

Biological Unit 1 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_076449	G	56	S	SPSY_HUMAN	Disease (MRXSSR)	121434610	A/B	G	56	S
2	UniProt	VAR_072748	F	58	L	SPSY_HUMAN	Disease (MRXSSR)	397515549	A/B	F	58	L
3	UniProt	VAR_071048	N	60	S	SPSY_HUMAN	Polymorphism	---	A/B	N	60	S
4	UniProt	VAR_076450	G	67	E	SPSY_HUMAN	Disease (MRXSSR)	397515550	A/B	G	67	E
5	UniProt	VAR_076451	V	132	G	SPSY_HUMAN	Disease (MRXSSR)	267607076	A/B	V	132	G
6	UniProt	VAR_076452	Y	328	C	SPSY_HUMAN	Disease (MRXSSR)	397515553	A/B	Y	328	C

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

Biological Unit 2 (3, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
4	UniProt	VAR_076450	G	67	E	SPSY_HUMAN	Disease (MRXSSR)	397515550	D	G	67	E
5	UniProt	VAR_076451	V	132	G	SPSY_HUMAN	Disease (MRXSSR)	267607076	C/D	V	132	G
6	UniProt	VAR_076452	Y	328	C	SPSY_HUMAN	Disease (MRXSSR)	397515553	C/D	Y	328	C

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPSY_HUMAN	122-362	4	A:122-362 B:122-362 C:122-362 D:122-362
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPSY_HUMAN	194-207	4	A:194-207 B:194-207 C:194-207 D:194-207

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPSY_HUMAN	122-362	2	A:122-362 B:122-362 - -
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPSY_HUMAN	194-207	2	A:194-207 B:194-207 - -

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.	SPSY_HUMAN	122-362	2	- - C:122-362 D:122-362
2	PABS_1	PS01330	Polyamine biosynthesis (PABS) domain signature.	SPSY_HUMAN	194-207	2	- - C:194-207 D:194-207

(no "Exon" information available for 3C6M)

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 SPSY_HUMAN | P52788 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:361
                                    13        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       303       313       323       333       343       353       363 
           SPSY_HUMAN     4 ARHSTLDFMLGAKADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEEIDSILNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKA 364
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c6mA01 A:4   -116 Siroheme synthase; domain 2                                                                   3c6mA02 A:117-172  [code=2.30.140.10, no name defined]  3c6mA03 A:173-364 Vaccinia Virus protein VP39                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..---hhhhhhhhhhhhhhh...eeeeee.....eeeeee.....eeeeeee...eeeeeee..----------hhhhhhhhhhhhhh.------......ee....................eeeeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhh..........eeeeee...hhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhh.ee..eeeee.hhhhhhhhhhhh...eeeeeee........------hhhhhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhhh.....eeeeeeee.hhhhh..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------S-L-S------E----------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------PABS_2  PDB: A:122-362 UniProt: 122-362                                                                                                                                                                                                          -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6m A   4 SRHSTLDFMLG---DGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQSY----------DSILNKVEERMKELS------VKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPIST------TWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKA 364
                                    13|   |   23        33        43        53        63        73  |      -   |    93       | -    |  113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283|      293       303       313       323       333       343       353       363 
                                     14  18                                                        76         87           101    108                                                                                                                                                                             284    291

Chain B from PDB  Type:PROTEIN  Length:342
 aligned with SPSY_HUMAN | P52788 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:362
                                    13        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       303       313       323       333       343       353       363  
           SPSY_HUMAN     4 ARHSTLDFMLGAKADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEEIDSILNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAK 365
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c6mB01 B:4     -116 Siroheme synthase; domain 2                                                                 3c6mB02 B:117-172  [code=2.30.140.10, no name defined]  3c6mB03 B:173-365 Vaccinia Virus protein VP39                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..-----hhhhhhhhhhhhh...eeeeeee...eeeeeee.....eeeeeee...eeeeeee.------hhhhhhhhhhhhhhhhhhhh-----.ee....ee....................eeeeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhh..........eeeeee...hhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh......ee..eeeee.hhhhhhhhhhhhh..eeeeeee.........----hhhhhhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhhh.....eeeeeeee........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------S-L-S------E----------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------PABS_2  PDB: B:122-362 UniProt: 122-362                                                                                                                                                                                                          --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PABS_1        -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6m B   4 SRHSTLDFMLG-----ETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQS------GKEEIDSILNKVEERMKELS-----RVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTS----STWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAK 365
                                    13|     | 23        33        43        53        63        73 |      83        93       | -   |   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 |    |293       303       313       323       333       343       353       363  
                                     14    20                                                     75     82                101   107                                                                                                                                                                               285  290

Chain C from PDB  Type:PROTEIN  Length:291
 aligned with SPSY_HUMAN | P52788 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:362
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364  
           SPSY_HUMAN     5 RHSTLDFMLGAKADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEEIDSILNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAKP 366
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c6mC01                                                        C:5-116      Siroheme synthase;         domain 2 3c6mC02 C:117-172  [code=2.30.140.10, no name defined]  3c6mC03 C:173-366 Vaccinia Virus protein VP39                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.-------------------------------------------------------.eeeeee.-----hhhhhhhhhhhhhhh...--------.ee..........................eeeeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhh...........eeeeee...hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh..........eeee..hhhhhhhhhhhhh..eeeeeee..........---hhhhhhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhhh.....eeeeeeee.hhhhh..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C-------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------PABS_2  PDB: C:122-362 UniProt: 122-362                                                                                                                                                                                                          ---- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PABS_1        --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6m C   5 RHSTLDFM-------------------------------------------------------LVLLDLQS-----QGKEEIDSILNKVEERMK--------RVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSP---STWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKAKP 366
                                   | -         -         -         -         -         -   |    74|     | 84        94   |     -  |    114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284 |   | 294       304       314       324       334       344       354       364  
                                  12                                                      68     75    81               98      107                                                                                                                                                                                286 290

Chain D from PDB  Type:PROTEIN  Length:278
 aligned with SPSY_HUMAN | P52788 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:361
                                    13        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       303       313       323       333       343       353       363 
           SPSY_HUMAN     4 ARHSTLDFMLGAKADGETILKGLQSIFQEQGMAESVHTWQDHGYLATYTNKNGSFANLRIYPHGLVLLDLQSYDGDAQGKEEIDSILNKVEERMKELSQDSTGRVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTSPEEDSTWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKA 364
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c6mD01 D:                                               4-116                                                   3c6mD02 D:117-172  [code=2.30.140.10, no name defined]  3c6mD03 D:173-364 Vaccinia Virus protein VP39                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..-----------------------------------------------.ee.....eeeee..-------------------------------.......ee....................eeeeeeeee....eeeeeee...eeeeee..eeeee..hhhhhhhhh..........eeeeee...hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhh.ee..eeee..hhhhhhhhhhhh...eeeeeee.........-----hhhhhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhhhh....eeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------E----------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------------PABS_2  PDB: D:122-362 UniProt: 122-362                                                                                                                                                                                                          -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PABS_1        ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6m D   4 SRHSTLDFML-----------------------------------------------LRIYPHGLVLLDLQS-------------------------------RVKRLPPIVRGGAIDRYWPTADGRLVEYDIDEVVYDEDSPYQNIKILHSKQFGNILILSGDVNLAESDLAYTRAIMGSGKEDYTGKDVLILGGGDGGILCEIVKLKPKMVTMVEIDQMVIDGCKKYMRKTCGDVLDNLKGDCYQVLIEDCIPVLKRYAKEGREFDYVINDLTAVPISTS-----TWEFLRLILDLSMKVLKQDGKYFTQGNCVNLTEALSLYEEQLGRLYCPVEFSKEIVCVPSYLELWVFYTVWKKA 364
                                    13         -         -         -         -       |63        73 |       -         -         -   |   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 |     293       303       313       323       333       343       353       363 
                                    13                                              61            75                             107                                                                                                                                                                               285   291

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 '\|'

(no "SCOP Domain" information available for 3C6M)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: Siroheme synthase; domain 2 (6)

Human (Homo sapiens) (2)

1a	3c6mA01	A:4-116
1b	3c6mB01	B:4-116
1c	3c6mC01	C:5-116

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Human (Homo sapiens) (49)

2a	3c6mC03	C:173-366
2b	3c6mB03	B:173-365
2c	3c6mD03	D:173-364
2d	3c6mA03	A:173-364

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)

Human (Homo sapiens) (2)

3a	3c6mA02	A:117-172
3b	3c6mB02	B:117-172
3c	3c6mC02	C:117-172
3d	3c6mD02	D:117-172

Architecture: Single Sheet (341)

Topology: spermine synthase fold (1)

Homologous Superfamily: spermine synthase domain (1)

Human (Homo sapiens) (1)

3c6mD01

D:4-116

(no "Pfam Domain" information available for 3C6M)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (SPSY_HUMAN | P52788)

molecular function
	GO:0016768	spermine synthase activity	Catalysis of the reaction: S-adenosylmethioninamine + spermidine = 5'-methylthioadenosine + spermine.
	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:0006555	methionine metabolic process	The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	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:0006597	spermine biosynthetic process	The chemical reactions and pathways resulting in the formation of spermine, a polybasic amine found in human sperm, in ribosomes and in some viruses and involved in nucleic acid packaging.
	GO:0008215	spermine metabolic process	The chemical reactions and pathways involving spermine, a polybasic amine found in human sperm, in ribosomes and in some viruses, which is involved in nucleic acid packaging. Synthesis is regulated by ornithine decarboxylase which plays a key role in control of DNA replication.
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.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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	3c6m
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	SPSY_HUMAN \| P52788
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	2.5.1.22
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	SPSY_HUMAN \| P52788
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UniProtKB/Swiss-Prot
	SPSY_HUMAN \| P52788	:	3c6k

3c6k	CRYSTAL STRUCTURE OF HUMAN SPERMINE SYNTHASE IN COMPLEX WITH SPERMIDINE AND 5-METHYLTHIOADENOSINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 17)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (4, 12)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File