3MC6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SCDPL1

Authors :   F. Bourquin, M. G. Grutter, G. Capitani

Date :   27 Mar 10 (Deposition) - 18 Aug 10 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.15

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

Keywords :   Carboxy-Lyase Activity, Pyridoxyl Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Bourquin, H. Riezman, G. Capitani, M. G. Grutter
Structure And Function Of Sphingosine-1-Phosphate Lyase, A Key Enzyme Of Sphingolipid Metabolism.
Structure V. 18 1054 2010
PubMed-ID: 20696404 | Reference-DOI: 10.1016/J.STR.2010.05.011

Molecule 1 - SPHINGOSINE-1-PHOSPHATE LYASE
	Chains	:	A
	EC Number	:	4.1.2.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE60
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 103-589
	Gene	:	BST1, D9819.5, DPL1, YDR294C
	Mutation	:	YES
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SP-LYASE, YSPL, SPHINGOSINE-1-PHOSPHATE ALDOLASE, BESTOWED OF SPHINGOSINE TOLERANCE 1

Molecule 2 - SPHINGOSINE-1-PHOSPHATE LYASE
	Chains	:	C
	EC Number	:	4.1.2.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE60
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 103-589
	Gene	:	BST1, D9819.5, DPL1, YDR294C
	Mutation	:	YES
	Organism Common	:	BREWER'S YEAST,LAGER BEER YEAST,YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SP-LYASE, YSPL, SPHINGOSINE-1-PHOSPHATE ALDOLASE, BESTOWED OF SPHINGOSINE TOLERANCE 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	LLP	1	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	LLP	-1	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
2	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:171 , ALA A:172 , TYR A:174 , LEU A:197 , HIS A:198 , LLP A:380	BINDING SITE FOR RESIDUE PO4 A 1
2	AC2	SOFTWARE	GLY C:235 , THR C:236 , ASP C:377 , HIS C:379 , GLY C:421 , SER C:422	BINDING SITE FOR RESIDUE PO4 C 1
3	AC3	SOFTWARE	GLY C:171 , ALA C:172 , TYR C:174 , HIS C:198 , PHE C:317 , LYS C:380 , LYS C:386	BINDING SITE FOR RESIDUE PO4 C 2

(no "SS Bond" information available for 3MC6)

Asymmetric Unit

No.	Residues
1	Ala A:314	-	Pro A:315
2	Lys A:507	-	Pro A:508
3	Ala C:314	-	Pro C:315
4	Lys C:507	-	Pro C:508

(no "SAP(SNP)/Variant" information available for 3MC6)

(no "PROSITE Motif" information available for 3MC6)

(no "Exon" information available for 3MC6)

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:426
 aligned with SGPL_YEAST | Q05567 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:449
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570         
           SGPL_YEAST   131 QLMNFPQLPSNGIPQDDVIEELNKLNDLIPHTQWKEGKVSGAVYHGGDDLIHLQTIAYEKYCVANQLHPDVFPAVRKMESEVVSMVLRMFNAPSDTGCGTTTSGGTESLLLACLSAKMYALHHRGITEPEIIAPVTAHAGFDKAAYYFGMKLRHVELDPTTYQVDLGKVKKFINKNTILLVGSAPNFPHGIADDIEGLGKIAQKYKLPLHVDSCLGSFIVSFMEKAGYKNLPLLDFRVPGVTSISCDTHKYGFAPKGSSVIMYRNSDLRMHQYYVNPAWTGGLYGSPTLAGSRPGAIVVGCWATMVNMGENGYIESCQEIVGAAMKFKKYIQENIPDLNIMGNPRYSVISFSSKTLNIHELSDRLSKKGWHFNALQKPVALHMAFTRLSAHVVDEICDILRTTVQELKSESNSKPSPDGTSALYGVAGSVKTAGVADKLIVGFLDALYK 579
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh....hhhhh.........hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhh..eeeee.............hhhhh...eeeeeee................hhhhhh...eeee...hhhhhhhhh..................eeeee...........eeee..hhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee....hhhhhhhhhhh.....ee......eeee.......hhhhhhhhhhhhhhhhh..-----------------------..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mc6 A 131 QLMNFPQLPSNGIPQDDVIEELNKLNDLIPHTQWKEGKVSGAVYHGGDDLIHLQTIAYEKYCVANQLHPDVFPAVRKMESEVVSMVLRMFNAPSDTGCGTTTSGGTESLLLACLSAKMYALHHRGITEPEIIAPVTAHAGFDKAAYYFGMKLRHVELDPTTYQVDLGKVKKFINKNTVLLVGSAPNFPHGIADDIEGLGKIAQKYKLPLHVDSCLGSFIVSFMEKAGYKNLPLLDFRVPGVTSISCDTHkYGFAPKGSSVIMYRNSDLRMHQYYVNPAWTGGLYGSPTLAGSRPGAIVVGCWATMVNMGENGYIESCQEIVGAAMKFKKYIQENIPDLDIMGNPRYSVISFSSKTLNIHELSDRLSKKGWHFNALQKPVALHMAFTRLSAHVVDEICDILRTTVQELKSE-----------------------GVADKLIVGFLDALYK 579
                                   140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540         -         -   |   570         
                                                                                                                                                                                                                                                                                   380-LLP                                                                                                                                                         540                     564

Chain C from PDB  Type:PROTEIN  Length:424
 aligned with SGPL_YEAST | Q05567 from UniProtKB/Swiss-Prot  Length:589

    Alignment length:450
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579
           SGPL_YEAST   130 SQLMNFPQLPSNGIPQDDVIEELNKLNDLIPHTQWKEGKVSGAVYHGGDDLIHLQTIAYEKYCVANQLHPDVFPAVRKMESEVVSMVLRMFNAPSDTGCGTTTSGGTESLLLACLSAKMYALHHRGITEPEIIAPVTAHAGFDKAAYYFGMKLRHVELDPTTYQVDLGKVKKFINKNTILLVGSAPNFPHGIADDIEGLGKIAQKYKLPLHVDSCLGSFIVSFMEKAGYKNLPLLDFRVPGVTSISCDTHKYGFAPKGSSVIMYRNSDLRMHQYYVNPAWTGGLYGSPTLAGSRPGAIVVGCWATMVNMGENGYIESCQEIVGAAMKFKKYIQENIPDLNIMGNPRYSVISFSSKTLNIHELSDRLSKKGWHFNALQKPVALHMAFTRLSAHVVDEICDILRTTVQELKSESNSKPSPDGTSALYGVAGSVKTAGVADKLIVGFLDALYK 579
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------Pyridoxal_deC-3mc6C01 C:139-484                                                                                                                                                                                                                                                                                                                           ----------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Pyridoxal_deC-3mc6C02 C:139-484                                                                                                                                                                                                                                                                                                                           ----------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..............hhhhhhhhhhhhhhh....hhhhh.........hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhh..eeeee.............hhhhh...eeeeeee................hhhhhh...eeee...hhhhhhhhh..................eeeee...........eeee..hhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeee....hhhhhhhhhhh.....ee......eeee.......hhhhhhhhhhhhhhhhh..--------------------------..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mc6 C 130 SQLMNFPQLPSNGIPQDDVIEELNKLNDLIPHTQWKEGKVSGAVYHGGDDLIHLQTIAYEKYCVANQLHPDVFPAVRKMESEVVSMVLRMFNAPSDTGCGTTTSGGTESLLLACLSAKMYALHHRGITEPEIIAPVTAHAGFDKAAYYFGMKLRHVELDPTTYQVDLGKVKKFINKNTVLLVGSAPNFPHGIADDIEGLGKIAQKYKLPLHVDSCLGSFIVSFMEKAGYKNLPLLDFRVPGVTSISCDTHKYGFAPKGSSVIMYRNSDLRMHQYYVNPAWTGGLYGSPTLAGSRPGAIVVGCWATMVNMGENGYIESCQEIVGAAMKFKKYIQENIPDLDIMGNPRYSVISFSSKTLNIHELSDRLSKKGWHFNALQKPVALHMAFTRLSAHVVDEICDILRTTVQELKSE--------------------------DKLIVGFLDALYK 579
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539|        -         -       569       579
                                                                                                                                                                                                                                                                                                                                                                                                                                                    540                        567

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 3MC6)

(no "CATH Domain" information available for 3MC6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Pyridoxal_deC (14)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (1)

1a	Pyridoxal_deC-3mc6C01	C:139-484
1b	Pyridoxal_deC-3mc6C02	C:139-484

Asymmetric Unit(hide GO term definitions)

Chain A,C (SGPL_YEAST | Q05567)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	GO:0008117	sphinganine-1-phosphate aldolase activity	Catalysis of the reaction: sphinganine 1-phosphate = phosphoethanolamine + palmitaldehyde.
biological process
	GO:0019722	calcium-mediated signaling	Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0009267	cellular response to starvation	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0006665	sphingolipid metabolic process	The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
cellular component
	GO:0032541	cortical endoplasmic reticulum	A cortical network of highly dynamic tubules that are juxtaposed to the plasma membrane and undergo ring closure and tubule-branching movements.
	GO:0097038	perinuclear endoplasmic reticulum	The portion of endoplasmic reticulum, the intracellular network of tubules and cisternae, that occurs near the nucleus. The lumen of the perinuclear endoplasmic reticulum is contiguous with the nuclear envelope lumen (also called perinuclear space), the region between the inner and outer nuclear membranes.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:314 - Pro A:315	[ RasMol ]
		Ala C:314 - Pro C:315	[ RasMol ]
		Lys A:507 - Pro A:508	[ RasMol ]
		Lys C:507 - Pro C:508	[ RasMol ]

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3mad	CRYSTAL STRUCTURE OF STSPL (SYMMETRIC FORM)
3maf	CRYSTAL STRUCTURE OF STSPL (SYMMETRIC FORM)
3mau	CRYSTAL STRUCTURE OF STSPL IN COMPLEX WITH PHOSPHOETHANOLAMINE
3mbb	CRYSTAL STRUCTURE OF STSPL (APO FORM, AFTER TREATMENT WITH SEMICARBAZIDE)

Description

Compounds

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Ligands, Modified Residues, Ions (2, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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