2CMH - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM HELICOBACTER PYLORI

Authors :   Y. -J. Sun, P. -K. Lu

Date :   08 May 06 (Deposition) - 08 May 07 (Release) - 20 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Putrescine Aminopropyltransferase, Spermidine Biosynthesis, Spee, Transferase, Spermidine Synthase, Helicobacter Pylori, Polyamine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. -K. Lu, J. -Y. Tsai, H. Y. Chien, H. Huang, C. -H. Chu, Y. -J. Sun
Crystal Structure Of Helicobacter Pylori Spermidine Synthase: A Rossmann-Like Fold With A Distinct Active Site
Proteins: Struct. , Funct. , V. 67 743 2007 Bioinf.
PubMed-ID: 17357156 | Reference-DOI: 10.1002/PROT.21315

Molecule 1 - SPERMIDINE SYNTHASE
	Chains	:	A, B, C
	EC Number	:	2.5.1.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-30
	Expression System Strain	:	SG13009
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	26695
	Synonym	:	PUTRESCINE AMINOPROPYLTRANSFERASE, SPDSY

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2CMH)

(no "Site" information available for 2CMH)

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

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

(no "SAP(SNP)/Variant" information available for 2CMH)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPEE_HELPY	1-249	3	A:1-249 B:1-249 C:1-249

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPEE_HELPY	1-249	4	- B:1-249 C:1-249

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PABS_2	PS51006	Polyamine biosynthesis (PABS) domain profile.	SPEE_HELPY	1-249	3	A:1-249 B:1-249 C:1-249

(no "Exon" information available for 2CMH)

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:262
 aligned with SPEE_HELPY | O25503 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           SPEE_HELPY     1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
               SCOP domains d2cmha_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..eeeeeee....eeeeeee...eeeeee..eeee...hhhhhhhhhhhhhh......eeeee...hhhhhhhhh....eeeee..hhhhhhh......hhhhhhh...eeee.hhhhh....eeeeee....hhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeee.........eeeeeee.........hhhhhh........hhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PABS_2  PDB: A:1-249 UniProt: 1-249                                                                                                                                                                                                                      ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmh A   1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
                                    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

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with SPEE_HELPY | O25503 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           SPEE_HELPY     1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
               SCOP domains d2cmhb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..eeeeeee....eeeeee.....eeeee..eeee...hhhhhhhhhhhhhh......eeeee...hhhhhhhhh....eeeee..hhhhhhh......hhhhhhh...eeee.hhhhh....eeeeee....hhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhh...eeeee..........eeeeee.........hhhhhhhh......hhhhhhhh...hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PABS_2  PDB: B:1-249 UniProt: 1-249                                                                                                                                                                                                                      ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmh B   1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
                                    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

Chain C from PDB  Type:PROTEIN  Length:262
 aligned with SPEE_HELPY | O25503 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:262
                                    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  
           SPEE_HELPY     1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
               SCOP domains d2cmhc_ C: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeee..eeeeeee....eeeeeee...eeeeee...eee..hhhhhhhhhhhhhhh......eeeee...hhhhhhhhh....eeeee..hhhhhhh......hhhhhhh...eeee.hhhhh....eeeeee....hhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhh...eeeee..........eeeeee.........hhhhhhhh......hhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PABS_2  PDB: C:1-249 UniProt: 1-249                                                                                                                                                                                                                      ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cmh C   1 MWITQEITPYLRKEYTIEAKLLDVRSEHNILEIFKSKDFGEIAMLNRQLLFKNFLHIESELLAHMGGCTKKELKEVLIVDGFDLELAHQLFKYDTHIDFVQADEKILDSFISFFPHFHEVKNNKNFTHAKQLLDLDIKKYDLIFCLQEPDIHRIDGLKRMLKEDGVFISVAKHPLLEHVSMQNALKNMGGVFSVAMPFVAPLRILSNKGYIYASFKTHPLKDLMTPKIEALTSVRYYNEDIHRAAFALPKNLQEVFKDNIKS 262
                                    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

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

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

Family: automated matches (94)

Protein domain: automated matches (94)

Helicobacter pylori [TaxId: 85962] (2)

1a	d2cmha_	A:
1b	d2cmhb_	B:
1c	d2cmhc_	C:

(no "CATH Domain" information available for 2CMH)

(no "Pfam Domain" information available for 2CMH)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SPEE_HELPY | O25503)

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: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: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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	Ligands, Modified Residues, Ions
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(no "Sites" information available for 2cmh)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cmh)

Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]

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	SPEE_HELPY \| O25503	:	2cmg

2cmg	CRYSTAL STRUCTURE OF SPERMIDINE SYNTHASE FROM HELICOBACTER PYLORI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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Gene Ontology (6, 6)

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