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(-) Description

Title :  CRYSTAL STRUCTURE OF AUTOTAXIN (ENPP2) WITH 7-ALPHA-HYDROXYCHOLESTEROL
 
Authors :  J. Hausmann, R. P. Joosten, A. Perrakis
Date :  07 Sep 15  (Deposition) - 13 Apr 16  (Release) - 27 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Autotaxin, Enpp2, Lpa, Steroids, Bile Salts, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. J. Keune, J. Hausmann, R. Bolier, D. Tolenaars, A. Kremer, T. Heidebrecht, R. P. Joosten, M. Sunkara, A. J. Morris, E. Matas-Rico W. H. Moolenaar, R. P. Oude Elferink, A. Perrakis
Steroid Binding To Autotaxin Links Bile Salts And Lysophosphatidic Acid Signalling.
Nat Commun V. 7 11248 2016
PubMed-ID: 27075612  |  Reference-DOI: 10.1038/NCOMMS11248

(-) Compounds

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
    Chains: A
    EC Number: 3.1.4.39
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: ENPP2, ATX, NPPS2
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: E-NPP 2,AUTOTAXIN,EXTRACELLULAR LYSOPHOSPHOLIPASE D,LYSOPLD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 38)

Asymmetric/Biological Unit (10, 38)
No.NameCountTypeFull Name
15JK1Ligand/Ion7ALPHA-HYDROXYCHOLESTEROL
2BMA1Ligand/IonBETA-D-MANNOSE
3CA1Ligand/IonCALCIUM ION
4GOL7Ligand/IonGLYCEROL
5IOD10Ligand/IonIODIDE ION
6NA2Ligand/IonSODIUM ION
7NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
8SCN11Ligand/IonTHIOCYANATE ION
9TPO1Mod. Amino AcidPHOSPHOTHREONINE
10ZN2Ligand/IonZINC ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETPO A:209 , ASP A:311 , HIS A:315 , HIS A:474 , HOH A:1236binding site for residue ZN A 904
02AC2SOFTWAREASP A:171 , TPO A:209 , ASP A:358 , HIS A:359binding site for residue ZN A 905
03AC3SOFTWARELEU A:78 , TYR A:214 , LYS A:248 , TRP A:254 , TRP A:260 , ILE A:261 , TRP A:275 , PHE A:777 , THR A:778 , SCN A:919 , HOH A:1002 , HOH A:1114binding site for residue 5JK A 906
04AC4SOFTWAREASP A:739 , ASN A:741 , ASP A:743 , LEU A:745 , ASP A:747 , HOH A:1318binding site for residue CA A 907
05AC5SOFTWAREASN A:230 , ARG A:391binding site for residue IOD A 908
06AC6SOFTWAREMET A:232 , ARG A:393binding site for residue IOD A 909
07AC7SOFTWAREARG A:162binding site for residue IOD A 910
08AC8SOFTWAREARG A:252binding site for residue IOD A 911
09AC9SOFTWAREGLN A:134 , HOH A:1287binding site for residue IOD A 912
10AD1SOFTWARELEU A:564 , PRO A:654binding site for residue IOD A 913
11AD2SOFTWAREASN A:576 , ASN A:582binding site for residue IOD A 914
12AD3SOFTWARELEU A:788binding site for residue IOD A 915
13AD4SOFTWAREASP A:782binding site for residue IOD A 916
14AD5SOFTWAREARG A:540 , SER A:846binding site for residue IOD A 917
15AD6SOFTWARETYR A:677 , LYS A:709binding site for residue SCN A 918
16AD7SOFTWARETRP A:260 , PHE A:273 , PHE A:274 , 5JK A:906 , HOH A:1307binding site for residue SCN A 919
17AD8SOFTWARELYS A:80 , VAL A:277 , SER A:278binding site for residue SCN A 920
18AD9SOFTWAREHIS A:281 , SER A:307 , ILE A:331 , THR A:334 , HOH A:1126binding site for residue SCN A 921
19AE1SOFTWARETYR A:496 , ARG A:535binding site for residue SCN A 922
20AE2SOFTWAREHIS A:225 , ARG A:252 , TRP A:253 , GLY A:255 , ARG A:439 , LYS A:637 , GOL A:935 , HOH A:1018binding site for residue SCN A 923
21AE3SOFTWAREPRO A:322 , THR A:607 , SER A:608 , ILE A:624binding site for residue SCN A 924
22AE4SOFTWARELYS A:80 , SER A:83 , SER A:84 , CYS A:85 , ASP A:90binding site for residue SCN A 926
23AE5SOFTWARETHR A:748 , GLU A:749binding site for residue SCN A 927
24AE6SOFTWARETYR A:669 , ASP A:672 , MET A:675 , GOL A:931 , HOH A:1357 , HOH A:1414binding site for residue NA A 928
25AE7SOFTWAREASN A:801 , SER A:804 , SER A:807 , HOH A:1361 , HOH A:1400 , HOH A:1438binding site for residue NA A 929
26AE8SOFTWAREPRO A:541 , THR A:542 , MET A:543binding site for residue GOL A 930
27AE9SOFTWARETYR A:669 , LYS A:670 , MET A:675 , SER A:676 , TYR A:677 , NA A:928binding site for residue GOL A 931
28AF1SOFTWAREPRO A:522 , NAG A:901 , NAG A:902 , HOH A:1105binding site for residue GOL A 932
29AF2SOFTWARECYS A:123 , GLY A:127 , ASP A:128 , CYS A:129 , LEU A:286 , LEU A:289 , GLY A:341 , GLN A:344 , LEU A:345binding site for residue GOL A 933
30AF3SOFTWAREPRO A:71 , PRO A:199 , TYR A:200binding site for residue GOL A 934
31AF4SOFTWAREHIS A:251 , ARG A:252 , TRP A:254 , LYS A:637 , SER A:725 , GLU A:726 , ASN A:728 , PHE A:777 , SCN A:923 , HOH A:1101binding site for residue GOL A 935
32AF5SOFTWAREPRO A:386 , GLY A:387 , HIS A:452 , VAL A:453 , ALA A:454 , LYS A:577 , HOH A:1007 , HOH A:1298 , HOH A:1403binding site for residue GOL A 936
33AF6SOFTWAREVAL A:447 , ARG A:449 , ASP A:477 , VAL A:480 , HOH A:1276 , HOH A:1284binding site for residue SCN A 937
34AF7SOFTWARELEU A:220 , PRO A:522 , ASN A:524 , LEU A:745 , HIS A:831 , GOL A:932 , HOH A:1001 , HOH A:1049 , HOH A:1054 , HOH A:1083 , HOH A:1120 , HOH A:1204 , HOH A:1211binding site for Poly-Saccharide residues NAG A 901 through BMA A 903 bound to ASN A 524

(-) SS Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1A:58 -A:75
2A:62 -A:93
3A:73 -A:86
4A:79 -A:85
5A:102 -A:119
6A:107 -A:137
7A:117 -A:130
8A:123 -A:129
9A:148 -A:194
10A:156 -A:350
11A:366 -A:468
12A:413 -A:805
13A:566 -A:666
14A:568 -A:651
15A:774 -A:784

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:70 -Pro A:71
2Tyr A:205 -Pro A:206
3Gln A:309 -Pro A:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DLT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DLT)

(-) Exons   (0, 0)

(no "Exon" information available for 5DLT)

(-) Sequences/Alignments

Asymmetric/Biological 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:796
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhh.........hhhhh..............hhhhhh....hhhhhhh...hhhhh..................eeeeeee..hhhhhhhh...hhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee...eeeeee........hhhhhhhhh........eeeee.hhhhhhhh.........eeeee....eee..........ee......hhhhh..eeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh...........hhhhhhh.......hhhhhhh.....ee.....eeeee....eeeee.....eeeeeeee.........hhhhh.........hhhhh.hhhhhhhh...eeee..hhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dlt A  56 GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKtFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCKVEPKNKLEEFNKRLHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYES 860
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   |   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455   ||  472       482       492       502       512       522       532       542       552       562     ||574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854      
                                                                                                                                                                                   209-TPO                                                                                                                                                                                                                                                   459|                                                                                                  568|                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                              467                                                                                                   571
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5DLT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DLT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DLT)

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)

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  ENPP2_RAT | Q64610
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ENPP2_RAT | Q64610: 2xr9 2xrg 5dlv 5dlw 5ijq 5ijs 5l0b 5l0e 5l0k 5lqq

(-) Related Entries Specified in the PDB File

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