4GTZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE ENPP1 IN COMPLEX WITH CMP

Authors :   K. Kato, H. Nishimasu, R. Ishitani, O. Nureki

Date :   29 Aug 12 (Deposition) - 07 Nov 12 (Release) - 07 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.19

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

Keywords :   Bone Mineralization, Phosphodiesterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kato, H. Nishimasu, S. Okudaira, E. Mihara, R. Ishitani, J. Takagi, J. Aoki, O. Nureki
Crystal Structure Of Enpp1, An Extracellular Glycoprotein Involved In Bone Mineralization And Insulin Signaling.
Proc. Natl. Acad. Sci. Usa V. 109 16876 2012
PubMed-ID: 23027977 | Reference-DOI: 10.1073/PNAS.1208017109

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2, ALKALINE PHOSPHODIESTERASE I
	Chains	:	A, B
	EC Number	:	3.1.4.39
	Engineered	:	YES
	Expression System Cell	:	MAMMALIAN CELLS
	Expression System Plasmid	:	MODIFIED PCDNA3.1
	Expression System Strain	:	HEK293S GNT1-
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 51-59, 92-905
	Gene	:	ENPP2, NPPS2, PDNP2, ENPP1, MCG_9001
	Mutation	:	YES
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	THE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905)
	Synonym	:	E-NPP 2, AUTOTAXIN, EXTRACELLULAR LYSOPHOSPHOLIPASE D, LYSOPLD, ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE 1, ISOFORM CRA_D

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 20)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	C5P	2	Ligand/Ion	CYTIDINE-5'-MONOPHOSPHATE
3	CA	2	Ligand/Ion	CALCIUM ION
4	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
5	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 9)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	C5P	1	Ligand/Ion	CYTIDINE-5'-MONOPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MAN	3	Ligand/Ion	ALPHA-D-MANNOSE
5	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
2	C5P	1	Ligand/Ion	CYTIDINE-5'-MONOPHOSPHATE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
5	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:267	BINDING SITE FOR RESIDUE NAG A 1007
02	AC2	SOFTWARE	ASN A:323 , VAL A:326	BINDING SITE FOR RESIDUE NAG A 1008
03	AC3	SOFTWARE	ASP A:200 , THR A:238 , PHE A:239 , ASN A:259 , LEU A:272 , LYS A:277 , TYR A:322 , TYR A:353 , ASP A:358 , HIS A:406 , HIS A:517 , ZN A:1010 , ZN A:1011	BINDING SITE FOR RESIDUE C5P A 1009
04	AC4	SOFTWARE	ASP A:200 , THR A:238 , ASP A:405 , HIS A:406 , C5P A:1009	BINDING SITE FOR RESIDUE ZN A 1010
05	AC5	SOFTWARE	ASP A:358 , HIS A:362 , HIS A:517 , C5P A:1009	BINDING SITE FOR RESIDUE ZN A 1011
06	AC6	SOFTWARE	ASP A:780 , ASP A:782 , ASP A:784 , ARG A:786 , TYR A:787 , ASP A:788	BINDING SITE FOR RESIDUE CA A 1012
07	AC7	SOFTWARE	ASN B:267	BINDING SITE FOR RESIDUE NAG B 1003
08	AC8	SOFTWARE	ASN B:323 , VAL B:326	BINDING SITE FOR RESIDUE NAG B 1004
09	AC9	SOFTWARE	ASP B:200 , THR B:238 , PHE B:239 , ASN B:259 , LEU B:272 , PHE B:303 , TYR B:322 , TYR B:353 , ASP B:358 , HIS B:362 , HIS B:406 , HIS B:517 , ZN B:1006 , ZN B:1007	BINDING SITE FOR RESIDUE C5P B 1005
10	BC1	SOFTWARE	ASP B:200 , THR B:238 , ASP B:405 , HIS B:406 , C5P B:1005	BINDING SITE FOR RESIDUE ZN B 1006
11	BC2	SOFTWARE	ASP B:358 , HIS B:362 , HIS B:517 , C5P B:1005	BINDING SITE FOR RESIDUE ZN B 1007
12	BC3	SOFTWARE	ASP B:780 , ASP B:782 , ASP B:784 , ARG B:786 , TYR B:787 , ASP B:788	BINDING SITE FOR RESIDUE CA B 1008
13	BC4	SOFTWARE	LEU A:249 , SER A:253 , HIS A:482 , PRO A:565 , ASN A:567 , ASP A:784 , ARG A:786 , LEU A:874 , SER B:802	BINDING SITE FOR LINKED RESIDUES A 1001 to 1006
14	BC5	SOFTWARE	TYR B:250 , HIS B:482 , PRO B:565 , ASN B:567 , ASP B:784 , ARG B:786 , LEU B:874	BINDING SITE FOR LINKED RESIDUES B 1001 to 1002

Asymmetric Unit

No.	Residues
1	A:177	-	A:223
2	A:185	-	A:397
3	A:413	-	A:512
4	A:462	-	A:848
5	A:596	-	A:652
6	A:607	-	A:706
7	A:609	-	A:691
8	A:818	-	A:828
9	B:177	-	B:223
10	B:185	-	B:397
11	B:413	-	B:512
12	B:462	-	B:848
13	B:596	-	B:652
14	B:607	-	B:706
15	B:609	-	B:691
16	B:818	-	B:828

Asymmetric Unit

No.	Residues
1	Tyr A:234	-	Pro A:235
2	Glu A:356	-	Pro A:357
3	Val A:444	-	Pro A:445
4	Thr A:601	-	Ser A:602
5	Lys A:647	-	Gln A:648
6	Tyr B:234	-	Pro B:235
7	Glu B:356	-	Pro B:357
8	Val B:444	-	Pro B:445
9	Lys B:647	-	Gln B:648

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

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

(no "Exon" information available for 4GTZ)

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:706
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeee...hhhhhhhhhhhhhhhhhhhhh.eee..ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee...hhhhhh.......hhhhhhhhh...ee..........................hhhhhhhhhhhhh.........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....ee.....eeehhhhhh....eeee.....eeee..........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee...........ee......hhhhh..eeee.......eee..ee..hhhhhhhhhhh............hhhhh..............eee..................hhhhhhhhh.....ee.....eeeeee...eeeeee....eeeeeeeee....................hhhhh.....eeeee..........hhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhh.eee..eee....eeeeeeeee............eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gtz A 170 KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNMRPMYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGMLMDGLKDLGLDKCLNLILISDHGMEQGSCKKYVYLNKYLGDVNNVKVVYGPAARLRPTDVPETYYSFNYEALAKNLSCREPNQHFRPYLKPFLPKRLHFAKSDRIEPLTFYLDPQWQLALNPSERKYCGSGFHGSDNLFSNMQALFIGYGPAFKHGAEVDSFENIEVYNLMCDLLGLIPAPNNGSHGSLNHLLKKPIYNPSHPKEEGFLSQCPIKSTSNDLGCTCDPEDDDIYHMTVPYGRPRILLKQHRVCLLQQQQFLTGYSLDLLMPLWASYTFLSNDSNCLYQDLRIPLSPVHKCSYYKSNSKLSYGFLTPPRLNHIYSEALLTSNIVPMYQSFQVIWHYLHDTLLQRYAHERNGINVVSGPVFDFDYDGRYDSLEILKQNSRVIRSQEILIPTHFFIVLTSCKQLSETPLECSALESSAYILPHRPDNIESCTHGKRESSWVEELLTLHRARVTDVELITGLSFYQDRQESVSELLRLKTHLPIFS 902
                                   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       589       599       609 ||    635       645       655       665       675     ||692       702       712       722   ||  736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   611|                                                  681|                                  726|                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    628                                                   689                                   731

Chain B from PDB  Type:PROTEIN  Length:697
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeee...hhhhhhhhhhhhhhhhhhhhh.eee..ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee...hhhhhh.......hhhhhhhhh...ee..........................hhhhhhhhhhhhh.........eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....ee.....eeehhhhhh....eeee.....eeee..........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee........ee......hhhhh..eeee.......eee..ee..hhhhhhhhhh.............hhhhh..............eee..................hhhhhhhh.....ee.....eeeeee...eeeeee....eeeeeeeee...................hhhhh..eeee..........hhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhh.eee..eee....eeeeeeeee............eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gtz B 170 KSWVEETCESIDTPECPAEFESPPTLLFSLDGFRAEYLHTWGGLLPVISKLKNCGTYTKNMRPMYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPLWYKGQPIWVTANHQEVKSGTYFWPGSDVEIDGILPDIYKVYNGSVPFEERILAVLEWLQLPSHERPHFYTLYLEEPDSSGHSHGPVSSEVIKALQKVDRLVGMLMDGLKDLGLDKCLNLILISDHGMEQGSCKKYVYLNKYLGDVNNVKVVYGPAARLRPTDVPETYYSFNYEALAKNLSCREPNQHFRPYLKPFLPKRLHFAKSDRIEPLTFYLDPQWQLALNPSYCGSGFHGSDNLFSNMQALFIGYGPAFKHGAEVDSFENIEVYNLMCDLLGLIPAPNNGSHGSLNHLLKKPIYNPSHPKEEGFLSQCPIKSTSNDLGCTCDPDDDIYHMTVPYGRPRILLKQHRVCLLQQQQFLTGYSLDLLMPLWASYTFLSNDNCLYQDLRIPLSPVHKCSYYKLSYGFLTPPRLNHIYSEALLTSNIVPMYQSFQVIWHYLHDTLLQRYAHERNGINVVSGPVFDFDYDGRYDSLEILKQNSRVIRSQEILIPTHFFIVLTSCKQLSETPLECSALESSAYILPHRPDNIESCTHGKRESSWVEELLTLHRARVTDVELITGLSFYQDRQESVSELLRLKTHLPIFS 902
                                   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       512       522       532       542       552       562       572       582       592       602       629       639       649       659       669       679 ||    697       707  ||   721    || 735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       
                                                                                                                                                                                                                                                                                                                                                                           507|                                                                                                 611|                                                 681|                 710|        726|                                                                                                                                                                           
                                                                                                                                                                                                                                                                                                                                                                            511                                                                                                  629                                                  690                  715         731

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 4GTZ)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:356 - Pro A:357	[ RasMol ]
		Glu B:356 - Pro B:357	[ RasMol ]
		Lys A:647 - Gln A:648	[ RasMol ]
		Lys B:647 - Gln B:648	[ RasMol ]
		Thr A:601 - Ser A:602	[ RasMol ]
		Tyr A:234 - Pro A:235	[ RasMol ]
		Tyr B:234 - Pro B:235	[ RasMol ]
		Val A:444 - Pro A:445	[ RasMol ]
		Val B:444 - Pro B:445	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	4gtz
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Access by UniProt ID/Accession number
	ENPP1_MOUSE \| P06802
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	ENPP2_MOUSE \| Q9R1E6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
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	G3X9S2_MOUSE \| G3X9S2
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	3.1.4.39
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	G3X9S2_MOUSE \| G3X9S2
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UniProtKB/Swiss-Prot
	ENPP1_MOUSE \| P06802	:	4b56 4gtw 4gtx 4gty
	ENPP2_MOUSE \| Q9R1E6	:	3nkm 3nkn 3nko 3nkp 3nkq 3nkr 3wav 3waw 3wax 3way 4gtw 4gtx 4gty 5hrt 5inh 5jvg 5lia
	G3X9S2_MOUSE \| G3X9S2	:	4gtw 4gtx 4gty

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 20)

Sites (14, 14)

SS Bonds (16, 16)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (57, 89)

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