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(-) Description

Title :  CRYSTAL STRUCTURE OF AUTOTAXIN (ENPP2) RE-REFINED
 
Authors :  J. Hausmann, R. P. Joosten, A. Perrakis
Date :  02 Mar 16  (Deposition) - 15 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Lysophosphatidylcholine, Somatomedin, Inflammation, Metastasis, Neuropathic Pain, Vascular Development, Neural Development (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hausmann, W. J. Keune, A. L. Hipgrave Ederveen, L. Van Zeijl, R. P. Joosten, A. Perrakis
Structural Snapshots Of The Catalytic Cycle Of The Phosphodiesterase Autotaxin.
J. Struct. Biol. V. 195 199 2016
PubMed-ID: 27268273  |  Reference-DOI: 10.1016/J.JSB.2016.06.002

(-) 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 Taxid: 9606
    Expression System Variant: FLP-IN
    Gene: ENPP2, ATX, NPPS2
    Organism Common: 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, 39)

Asymmetric/Biological Unit (10, 39)
No.NameCountTypeFull Name
15JK1Ligand/Ion7ALPHA-HYDROXYCHOLESTEROL
2BMA1Ligand/IonBETA-D-MANNOSE
3CA1Ligand/IonCALCIUM ION
4GOL1Ligand/IonGLYCEROL
5IOD24Ligand/IonIODIDE ION
6NA2Ligand/IonSODIUM ION
7NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PO41Ligand/IonPHOSPHATE ION
9SCN4Ligand/IonTHIOCYANATE ION
10ZN2Ligand/IonZINC ION

(-) Sites  (30, 30)

Asymmetric Unit (30, 30)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:78 , SER A:81 , TYR A:214 , HIS A:251 , TRP A:254 , TRP A:260 , PHE A:274 , PHE A:777 , THR A:778 , HOH A:1002binding site for residue 5JK A 901
02AC2SOFTWARETYR A:677 , LYS A:709binding site for residue SCN A 905
03AC3SOFTWAREASP A:311 , HIS A:315 , HIS A:474 , PO4 A:908binding site for residue ZN A 906
04AC4SOFTWAREASP A:171 , THR A:209 , ASP A:358 , HIS A:359 , PO4 A:908binding site for residue ZN A 907
05AC5SOFTWAREASP A:171 , THR A:209 , ASN A:230 , LEU A:243 , ASP A:311 , HIS A:315 , HIS A:474 , LYS A:583 , ZN A:906 , ZN A:907binding site for residue PO4 A 908
06AC6SOFTWAREASP A:739 , ASN A:741 , ASP A:743 , LEU A:745 , ASP A:747 , HOH A:1142binding site for residue CA A 909
07AC7SOFTWAREASN A:230binding site for residue IOD A 910
08AC8SOFTWARELEU A:788binding site for residue IOD A 911
09AC9SOFTWARELYS A:709binding site for residue IOD A 912
10AD1SOFTWARESER A:278binding site for residue IOD A 915
11AD2SOFTWARESER A:846binding site for residue IOD A 916
12AD3SOFTWARETYR A:496 , ARG A:535binding site for residue IOD A 917
13AD4SOFTWAREHIS A:281 , SER A:307 , THR A:334 , HOH A:1255binding site for residue IOD A 918
14AD5SOFTWAREHIS A:251binding site for residue IOD A 919
15AD6SOFTWAREASP A:782binding site for residue IOD A 920
16AD7SOFTWARELYS A:709binding site for residue IOD A 924
17AD8SOFTWAREPHE A:160 , VAL A:161 , ARG A:162binding site for residue IOD A 925
18AD9SOFTWAREASN A:665binding site for residue IOD A 926
19AE1SOFTWARETRP A:253 , IOD A:938binding site for residue IOD A 927
20AE2SOFTWARELEU A:564binding site for residue IOD A 929
21AE3SOFTWAREGLN A:134binding site for residue IOD A 930
22AE4SOFTWAREARG A:174 , ASN A:481binding site for residue IOD A 931
23AE5SOFTWARETYR A:669 , ASP A:672 , MET A:675 , GOL A:939binding site for residue NA A 933
24AE6SOFTWAREASN A:801 , SER A:804 , SER A:807 , HOH A:1148 , HOH A:1204binding site for residue NA A 934
25AE7SOFTWARESER A:176 , LYS A:180 , PHE A:320binding site for residue SCN A 935
26AE8SOFTWARELYS A:80 , SER A:83 , SER A:84 , CYS A:85 , ASP A:90binding site for residue SCN A 936
27AE9SOFTWAREGLN A:309 , ASN A:326 , PRO A:327binding site for residue SCN A 937
28AF1SOFTWAREASN A:437 , IOD A:927binding site for residue IOD A 938
29AF2SOFTWARETYR A:669 , MET A:675 , SER A:676 , NA A:933binding site for residue GOL A 939
30AF3SOFTWAREPRO A:522 , ASN A:524 , LEU A:745 , HIS A:831 , HOH A:1001 , HOH A:1027 , HOH A:1039 , HOH A:1065 , HOH A:1074 , HOH A:1222binding site for Poly-Saccharide residues NAG A 902 through BMA A 904 bound to ASN A 524

(-) SS Bonds  (14, 14)

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: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 5IJQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IJQ)

(-) 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:783
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................hhhhhh.........hhhhh........................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........hhhhh.......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
                 5ijq A  56 GSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSIYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDKLEEFNKRLHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 859
                                    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 ||    409       419       429       439       449       469       479       489       499       509       519       529       539       549       559       569|      586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856   
                                                                                                                                                                                                                                                                                                                                                                               397|                                                    457|                                                                                                  569|                                                                                                                                                                                                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                402                                                     468                                                                                                   577
   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 5IJQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)

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  5ijq
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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 5dlt 5dlv 5dlw 5ijs 5l0b 5l0e 5l0k 5lqq

(-) Related Entries Specified in the PDB File

2xr9 THE ZN ATOMS WERE REFINED WITH ANISOTROPIC B-FACTORS TO STUDY THEIR MOVEMENT. ADDITIONAL MODEL CHANGES WERE INCLUSION OF A PREVIOUSLY UNIDENTIFIED 7-ALPHA-OXYSTEROL AND TWO SODIUM IONS.