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Title :   SOLUTION STRUCTURE OF THE SOMATOMEDIN B DOMAIN OF HUMAN ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER

Authors :   H. Abe, A. Sasagawa, N. Tochio, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   03 Apr 07 (Deposition) - 09 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   E-Npp 1, Phosphodiesterase I/Nucleotide Pyrophosphatase 1, Plasma-Cell Membrane Glycoprotein Pc-1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Abe, A. Sasagawa, N. Tochio, T. Tomizawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The Somatomedin B Domain Of Human Ectonucleotide Pyrophosphatase/Phosphodiesterase Family Member
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1
	Chains	:	A
	EC Number	:	3.1.4.1, 3.6.1.9
	Engineered	:	YES
	Expression System Plasmid	:	P050118-03
	Expression System Vector Type	:	PLASMID
	Fragment	:	SOMATOMEDIN_B
	Gene	:	ENPP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	'ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 1, E-NPP 1, PHOSPHODIESTERASE I/NUCLEOTIDE PYROPHOSPHATASE 1, PLASMA-CELL MEMBRANE GLYCOPROTEIN PC-1


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2YS0)

(no "Site" information available for 2YS0)

NMR Structure

No.	Residues
1	A:10	-	A:27
2	A:15	-	A:45
3	A:25	-	A:38
4	A:31	-	A:37

(no "Cis Peptide Bond" information available for 2YS0)

NMR Structure (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_070782	C	149	S	ENPP1_HUMAN	Disease (COLED)	397518477	A	C	10	S
2	UniProt	VAR_070783	C	164	S	ENPP1_HUMAN	Disease (COLED)	397518476	A	C	25	S
3	UniProt	VAR_008873	K	173	Q	ENPP1_HUMAN	Polymorphism	1044498	A	Q	34	Q
4	UniProt	VAR_077258	C	177	S	ENPP1_HUMAN	Disease (COLED)	---	A	C	38	S
5	UniProt	VAR_070784	C	177	Y	ENPP1_HUMAN	Disease (COLED)	397518475	A	C	38	Y
6	UniProt	VAR_037432	N	179	S	ENPP1_HUMAN	Polymorphism	2273411	A	N	40	S

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

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SMB_2	PS50958	Somatomedin B (SMB) domain profile.	ENPP1_HUMAN	104-144 145-189	1	- A:8-50
2	SMB_1	PS00524	Somatomedin B domain (SMB) signature.	ENPP1_HUMAN	120-140 164-184	1	- A:25-45

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000360971	1a	ENSE00002158232	chr6:132129156-132129415	260	ENPP1_HUMAN	1-80	80	1	A:1-7	7
1.2	ENST00000360971	2	ENSE00002156802	chr6:132168916-132168988	73	ENPP1_HUMAN	81-105	25	0	-	-
1.3	ENST00000360971	3	ENSE00002150919	chr6:132171130-132171246	117	ENPP1_HUMAN	105-144	40	0	-	-
1.4a	ENST00000360971	4a	ENSE00001147089	chr6:132172282-132172407	126	ENPP1_HUMAN	144-186	43	1	A:8-47	40
1.5	ENST00000360971	5	ENSE00001147082	chr6:132173315-132173375	61	ENPP1_HUMAN	186-206	21	1	A:47-56 (gaps)	21
1.6	ENST00000360971	6	ENSE00001147074	chr6:132176066-132176163	98	ENPP1_HUMAN	206-239	34	1	A:56-56	1
1.7	ENST00000360971	7	ENSE00000763739	chr6:132179808-132179887	80	ENPP1_HUMAN	239-265	27	0	-	-
1.8	ENST00000360971	8	ENSE00000763737	chr6:132181527-132181646	120	ENPP1_HUMAN	266-305	40	0	-	-
1.9a	ENST00000360971	9a	ENSE00000763735	chr6:132182735-132182844	110	ENPP1_HUMAN	306-342	37	0	-	-
1.10	ENST00000360971	10	ENSE00002189940	chr6:132185646-132185711	66	ENPP1_HUMAN	342-364	23	0	-	-
1.11a	ENST00000360971	11a	ENSE00000763731	chr6:132186006-132186078	73	ENPP1_HUMAN	364-388	25	0	-	-
1.12	ENST00000360971	12	ENSE00002149800	chr6:132189158-132189266	109	ENPP1_HUMAN	389-425	37	0	-	-
1.13	ENST00000360971	13	ENSE00002199824	chr6:132190498-132190629	132	ENPP1_HUMAN	425-469	45	0	-	-
1.14	ENST00000360971	14	ENSE00002185848	chr6:132193210-132193241	32	ENPP1_HUMAN	469-479	11	0	-	-
1.15	ENST00000360971	15	ENSE00002148681	chr6:132194063-132194190	128	ENPP1_HUMAN	480-522	43	0	-	-
1.16	ENST00000360971	16	ENSE00002152556	chr6:132195408-132195477	70	ENPP1_HUMAN	522-545	24	0	-	-
1.17	ENST00000360971	17	ENSE00002200104	chr6:132196916-132197003	88	ENPP1_HUMAN	546-575	30	0	-	-
1.18a	ENST00000360971	18a	ENSE00002173905	chr6:132198132-132198301	170	ENPP1_HUMAN	575-631	57	0	-	-
1.19	ENST00000360971	19	ENSE00002168137	chr6:132199682-132199733	52	ENPP1_HUMAN	632-649	18	0	-	-
1.20	ENST00000360971	20	ENSE00002179244	chr6:132201020-132201174	155	ENPP1_HUMAN	649-700	52	0	-	-
1.21	ENST00000360971	21	ENSE00002158282	chr6:132203485-132203614	130	ENPP1_HUMAN	701-744	44	0	-	-
1.22	ENST00000360971	22	ENSE00002177765	chr6:132204834-132204914	81	ENPP1_HUMAN	744-771	28	0	-	-
1.23	ENST00000360971	23	ENSE00002165145	chr6:132206071-132206203	133	ENPP1_HUMAN	771-815	45	0	-	-
1.24	ENST00000360971	24	ENSE00002180154	chr6:132207702-132207864	163	ENPP1_HUMAN	815-869	55	0	-	-
1.25b	ENST00000360971	25b	ENSE00001388381	chr6:132211481-132216295	4815	ENPP1_HUMAN	870-925	56	0	-	-

NMR Structure

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:56
 aligned with ENPP1_HUMAN | P22413 from UniProtKB/Swiss-Prot  Length:925

    Alignment length:197
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
          ENPP1_HUMAN    10 GSRGGEGGRAPREGPAGNGRDRGRSHAAEAPGDPQAAASLLAPMDVGEEPLEKAARARTAKDPNTYKVLSLVLSVCVLTTILGCIFGLKPSCAKEVKSCKGRCFERTFGNCRCDAACVELGNCCLDYQETCIEPEHIWTCNKFRCGEKRLTRSLCACSDDCKDKGDCCINYSSVCQGEKSWVEEPCESINEPQCPAG 206
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------Somatomedin_B-2ys0A01 A:8-50               ----------------- Pfam domains
         Sec.struct. author .......----------------------------------------------------------------------------------------------------------------------------------....................hhhhhhhh....hhhhhh.....---------...--... Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------------------------------------------------------------------------------------------------S--------------S--------Q---S-S--------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------Y----------------------------- SAPs(SNPs) (2)
                PROSITE (1) ----------------------------------------------------------------------------------------------SMB_2  PDB: - UniProt: 104-144           SMB_2  PDB: A:8-50 UniProt: 145-189          ----------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------SMB_1  PDB: -        -----------------------SMB_1  PDB: A:25-45  ---------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:1-7 UniProt: 1-80 [INCOMPLETE]                       Exon 1.2  PDB: -         --------------------------------------Exon 1.4a  PDB: A:8-47 UniProt: 144-186    -------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.3  PDB: - UniProt: 105-144       -----------------------------------------Exon 1.5              Transcript 1 (2)
                 2ys0 A   1 GSSGSSG----------------------------------------------------------------------------------------------------------------------------------WTCNKFRCGEKRLTRSLCACSDDCKDQGDCCINYSSVCQGEKS---------SGP--SSG  56
                                  |  -         -         -         -         -         -         -         -         -         -         -         -         -       |10        20        30        40        50        51 |  |  
                                  7                                                                                                                                  8                                        50        51 | 54  
                                                                                                                                                                                                                          53

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 2YS0)

(no "CATH Domain" information available for 2YS0)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Somatomedin_B] (13)

Family: Somatomedin_B (13)

Homo sapiens (Human) (5)

Somatomedin_B-2ys0A01

A:8-50

NMR Structure(hide GO term definitions)

Chain A (ENPP1_HUMAN | P22413)

molecular function
	GO:0050656	3'-phosphoadenosine 5'-phosphosulfate binding	Interacting selectively and non-covalently with 3'-phosphoadenosine 5'-phosphosulfate (PAPS), a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0035529	NADH pyrophosphatase activity	Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0005158	insulin receptor binding	Interacting selectively and non-covalently with the insulin receptor.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0047429	nucleoside-triphosphate diphosphatase activity	Catalysis of the reaction: H2O + a nucleoside triphosphate = diphosphate + a nucleotide.
	GO:0004551	nucleotide diphosphatase activity	Catalysis of the reaction: a dinucleotide + H2O = 2 mononucleotides.
	GO:0004528	phosphodiesterase I activity	Catalysis of the sequential hydrolytic removal of 5'-nucleotides from the 3'-hydroxy termini of 3'-hydroxy-terminated oligonucleotides.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
	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).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0005044	scavenger receptor activity	Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0050427	3'-phosphoadenosine 5'-phosphosulfate metabolic process	The chemical reactions and pathways involving 3'-phosphoadenosine 5'-phosphosulfate, a naturally occurring mixed anhydride. It is an intermediate in the formation of a variety of sulfo compounds in biological systems.
	GO:0031214	biomineral tissue development	Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation.
	GO:0030643	cellular phosphate ion homeostasis	Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell.
	GO:0032869	cellular response to insulin stimulus	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 insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0006091	generation of precursor metabolites and energy	The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0030505	inorganic diphosphate transport	The directed movement of inorganic diphosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0045599	negative regulation of fat cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
	GO:0046325	negative regulation of glucose import	Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
	GO:0045719	negative regulation of glycogen biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
	GO:0046627	negative regulation of insulin receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
	GO:0031953	negative regulation of protein autophosphorylation	Any process that stops, prevents or decreases the rate of the phosphorylation by a protein of one or more of its own residues.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0009143	nucleoside triphosphate catabolic process	The chemical reactions and pathways resulting in the breakdown of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
	GO:0006796	phosphate-containing compound metabolic process	The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
	GO:0006898	receptor-mediated endocytosis	An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
	GO:0030500	regulation of bone mineralization	Any process that modulates the frequency, rate or extent of bone mineralization.
	GO:0006771	riboflavin metabolic process	The chemical reactions and pathways involving riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
	GO:0030730	sequestering of triglyceride	The process of binding or confining any triester of glycerol such that it is separated from other components of a biological system.
cellular component
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0005887	integral component of plasma membrane	The component of the plasma 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:0005765	lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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