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Title :   CRYSTAL STRUCTURE OF SAPOSIN A IN COMPLEX WITH LAURYLDIMETHYLAMINE-N-OXIDE (LDAO)

Authors :   K. Popovic, G. G. Prive

Date :   18 Jan 12 (Deposition) - 15 Feb 12 (Release) - 14 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Saposin Fold, Sphingolipid Activator Protein, Galactosylceramide, Lauryldimethylamine-N-Oxide, Lipid, Detergent, Lysosome, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Popovic, J. Holyoake, R. Pomes, G. G. Prive
Structure Of Saposin A Lipoprotein Discs.
Proc. Natl. Acad. Sci. Usa V. 109 2908 2012
PubMed-ID: 22308394 | Reference-DOI: 10.1073/PNAS.1115743109

Molecule 1 - SAPOSIN-A
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 60-140
	Gene	:	PSAP, GLBA, SAP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 20)

No.	Name	Count	Type	Full Name
1	LDA	20	Ligand/Ion	LAURYL DIMETHYLAMINE-N-OXIDE

Biological Unit 1 (1, 40)

No.	Name	Count	Type	Full Name
1	LDA	40	Ligand/Ion	LAURYL DIMETHYLAMINE-N-OXIDE

Biological Unit 2 (1, 20)

No.	Name	Count	Type	Full Name
1	LDA	20	Ligand/Ion	LAURYL DIMETHYLAMINE-N-OXIDE

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:30 , THR A:34 , TRP A:37	BINDING SITE FOR RESIDUE LDA A 101
02	AC2	SOFTWARE	ASP A:20 , THR A:23 , GLU A:26 , LDA A:103 , LDA A:109	BINDING SITE FOR RESIDUE LDA A 102
03	AC3	SOFTWARE	GLU A:26 , TYR A:30 , LDA A:102 , LDA A:109	BINDING SITE FOR RESIDUE LDA A 103
04	AC4	SOFTWARE	LEU A:76 , ASN A:77 , LDA A:106 , LDA A:114 , LDA A:117	BINDING SITE FOR RESIDUE LDA A 104
05	AC5	SOFTWARE	TYR A:54 , ALA A:75 , ASN A:77 , LDA A:110 , LDA A:117 , LDA A:118	BINDING SITE FOR RESIDUE LDA A 105
06	AC6	SOFTWARE	VAL A:10 , LDA A:104 , LDA A:115 , HOH A:232	BINDING SITE FOR RESIDUE LDA A 106
07	AC7	SOFTWARE	TYR A:30 , LDA A:108 , LDA A:109 , HOH A:252	BINDING SITE FOR RESIDUE LDA A 107
08	AC8	SOFTWARE	LDA A:107 , LDA A:114 , LDA A:119	BINDING SITE FOR RESIDUE LDA A 108
09	AC9	SOFTWARE	LDA A:102 , LDA A:103 , LDA A:107 , LDA A:119	BINDING SITE FOR RESIDUE LDA A 109
10	BC1	SOFTWARE	ALA A:75 , LDA A:105	BINDING SITE FOR RESIDUE LDA A 110
11	BC2	SOFTWARE	GLU A:65 , GLU A:71 , LDA A:112 , LDA A:113 , LDA A:116 , HOH A:253	BINDING SITE FOR RESIDUE LDA A 111
12	BC3	SOFTWARE	LDA A:111 , LDA A:116 , LDA A:119	BINDING SITE FOR RESIDUE LDA A 112
13	BC4	SOFTWARE	VAL A:10 , MET A:66 , LDA A:111 , LDA A:115 , LDA A:119	BINDING SITE FOR RESIDUE LDA A 113
14	BC5	SOFTWARE	TRP A:37 , LDA A:104 , LDA A:108 , LDA A:117	BINDING SITE FOR RESIDUE LDA A 114
15	BC6	SOFTWARE	LEU A:38 , MET A:43 , LDA A:106 , LDA A:113 , LDA A:117 , LDA A:120	BINDING SITE FOR RESIDUE LDA A 115
16	BC7	SOFTWARE	LDA A:111 , LDA A:112	BINDING SITE FOR RESIDUE LDA A 116
17	BC8	SOFTWARE	THR A:34 , TRP A:37 , CYS A:47 , VAL A:51 , LDA A:104 , LDA A:105 , LDA A:114 , LDA A:115	BINDING SITE FOR RESIDUE LDA A 117
18	BC9	SOFTWARE	GLU A:25 , LEU A:28 , GLU A:32 , TYR A:54 , ILE A:61 , LDA A:105	BINDING SITE FOR RESIDUE LDA A 118
19	CC1	SOFTWARE	MET A:17 , LEU A:18 , LDA A:108 , LDA A:109 , LDA A:112 , LDA A:113	BINDING SITE FOR RESIDUE LDA A 119
20	CC2	SOFTWARE	ASP A:9 , LDA A:115	BINDING SITE FOR RESIDUE LDA A 120

Asymmetric Unit

No.	Residues
1	A:4	-	A:79
2	A:7	-	A:73
3	A:35	-	A:47

Asymmetric Unit

No.	Residues
1	Lys A:40	-	Pro A:41

(no "SAP(SNP)/Variant" information available for 4DDJ)

(no "PROSITE Motif" information available for 4DDJ)

Asymmetric Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000394936	1a	ENSE00001858117	chr10:73611126-73610939	188	SAP_HUMAN	1-14	14	0	-	-
1.2	ENST00000394936	2	ENSE00001239781	chr10:73594262-73594129	134	SAP_HUMAN	14-58	45	0	-	-
1.3	ENST00000394936	3	ENSE00000987087	chr10:73591677-73591603	75	SAP_HUMAN	59-83	25	1	A:1-24	24
1.4b	ENST00000394936	4b	ENSE00000987088	chr10:73591008-73590883	126	SAP_HUMAN	84-125	42	1	A:25-66	42
1.5	ENST00000394936	5	ENSE00001239733	chr10:73588834-73588634	201	SAP_HUMAN	126-192	67	1	A:67-80	14
1.6	ENST00000394936	6	ENSE00000987090	chr10:73587914-73587771	144	SAP_HUMAN	193-240	48	0	-	-
1.7	ENST00000394936	7	ENSE00000987091	chr10:73585650-73585594	57	SAP_HUMAN	241-259	19	0	-	-
1.10c	ENST00000394936	10c	ENSE00001239711	chr10:73581764-73581633	132	SAP_HUMAN	260-303	44	0	-	-
1.11	ENST00000394936	11	ENSE00000987093	chr10:73580092-73579997	96	SAP_HUMAN	304-335	32	0	-	-
1.12b	ENST00000394936	12b	ENSE00000987094	chr10:73579657-73579471	187	SAP_HUMAN	336-398	63	0	-	-
1.13	ENST00000394936	13	ENSE00000987095	chr10:73579379-73579222	158	SAP_HUMAN	398-450	53	0	-	-
1.14b	ENST00000394936	14b	ENSE00000987096	chr10:73578868-73578788	81	SAP_HUMAN	451-477	27	0	-	-
1.15b	ENST00000394936	15b	ENSE00000987097	chr10:73578481-73578374	108	SAP_HUMAN	478-513	36	0	-	-
1.16e	ENST00000394936	16e	ENSE00001917960	chr10:73577233-73576055	1179	SAP_HUMAN	514-524	11	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:80
 aligned with SAP_HUMAN | P07602 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:80
                                    69        79        89        99       109       119       129       139
            SAP_HUMAN    60 SLPCDICKDVVTAAGDMLKDNATEEEILVYLEKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCE 139
               SCOP domains d4ddja_ A: Saposin C                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: A:1-24   Exon 1.4b  PDB: A:25-66 UniProt: 84-125   Exon 1.5       Transcript 1
                 4ddj A   1 SLPCDICKDVVTAAGDMLKDNATEEEILVYLEKTCDWLPKPNMSASCKEIVDSYLPVILDIIKGEMSRPGEVCSALNLCE  80
                                    10        20        30        40        50        60        70        80

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: All alpha proteins (14657)

Fold: Saposin-like (21)

Superfamily: Saposin (17)

Family: NKL-like (13)

Protein domain: Saposin C (11)

Human (Homo sapiens) [TaxId: 9606] (11)

d4ddja_

(no "CATH Domain" information available for 4DDJ)

(no "Pfam Domain" information available for 4DDJ)

Asymmetric Unit(hide GO term definitions)

Chain A (SAP_HUMAN | P07602)

molecular function
	GO:0001664	G-protein coupled receptor binding	Interacting selectively and non-covalently with a G-protein coupled receptor.
	GO:0008047	enzyme activator activity	Binds to and increases the activity of an enzyme.
	GO:0008289	lipid binding	Interacting selectively and non-covalently with a lipid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007193	adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway	The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through inhibition of adenylyl cyclase activity and a subsequent decrease in the concentration of cyclic AMP (cAMP).
	GO:0071310	cellular response to organic substance	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 an organic substance stimulus.
	GO:0048589	developmental growth	The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
	GO:0060742	epithelial cell differentiation involved in prostate gland development	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell of the prostate gland.
	GO:0006687	glycosphingolipid metabolic process	The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
	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:0006869	lipid transport	The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:1903206	negative regulation of hydrogen peroxide-induced cell death	Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-induced cell death.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0060736	prostate gland growth	The increase in size or mass of the prostate gland where the increase in size or mass has the specific outcome of the progression of the gland, from its formation to its mature state.
	GO:0043408	regulation of MAPK cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
	GO:0010506	regulation of autophagy	Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:0019216	regulation of lipid metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0043202	lysosomal lumen	The volume enclosed within the lysosomal membrane.
	GO:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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	SAP_HUMAN \| P07602	:	1m12 1n69 1sn6 2dob 2gtg 2qyp 2r0r 2r1q 2rb3 2z9a 3bqp 3bqq 4uex 4v2o

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