PDE_NAJAT
ID PDE_NAJAT Reviewed; 830 AA.
AC A0A2D0TC04;
DT 16-OCT-2019, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2017, sequence version 1.
DT 03-AUG-2022, entry version 15.
DE RecName: Full=Venom phosphodiesterase {ECO:0000303|Ref.1};
DE Short=PDE {ECO:0000303|Ref.1};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:W8E7D1};
OS Naja atra (Chinese cobra).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera;
OC Serpentes; Colubroidea; Elapidae; Elapinae; Naja.
OX NCBI_TaxID=8656;
RN [1] {ECO:0000312|PDB:5GZ4, ECO:0000312|PDB:5GZ5}
RP X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) IN COMPLEX WITH ZINC AND AMP, ACTIVE
RP SITE, GLYCOSYLATION AT ASN-16; ASN-193; ASN-236; ASN-247; ASN-489; ASN-723
RP AND ASN-742, AND DISULFIDE BOND.
RA Lin C.C., Wu B.S., Wu W.G.;
RT "Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra
RT (Naja atra atra) in complex with AMP.";
RL Submitted (SEP-2016) to the PDB data bank.
CC -!- FUNCTION: Hydrolyzes ADP with high activity. Shows weak or no activity
CC on 5'-AMP, 5'-GMP, 3'-AMP, ATP, cAMP, and cGMP. Is devoid of
CC monophosphatase and proteinase activities. Dose-dependently inhibits
CC platelet aggregation induced by ADP and collagen.
CC {ECO:0000250|UniProtKB:W8E7D1}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ADP + H2O = AMP + H(+) + phosphate; Xref=Rhea:RHEA:61436,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:456215, ChEBI:CHEBI:456216;
CC Evidence={ECO:0000250|UniProtKB:W8E7D1};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:W8E7D1};
CC Note=Binds 2 divalent metal cations per subunit. {ECO:0000269|Ref.1,
CC ECO:0007744|PDB:5GZ4, ECO:0007744|PDB:5GZ5};
CC -!- SUBUNIT: Monomer cleaved in two subunits; disulfide-linked. Is
CC synthesized as a single-chain protein and is subsequently cleaved to
CC form a two-subunit protein held together with disulfide bonds.
CC {ECO:0000250|UniProtKB:W8E7D1}.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000250|UniProtKB:W8E7D1}.
CC -!- TISSUE SPECIFICITY: Expressed by venom gland. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the nucleotide pyrophosphatase/phosphodiesterase
CC family. {ECO:0000305}.
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DR PDB; 5GZ4; X-ray; 2.55 A; A=1-830.
DR PDB; 5GZ5; X-ray; 2.09 A; A=1-830.
DR PDB; 7CBA; X-ray; 2.90 A; A/B=1-830.
DR PDBsum; 5GZ4; -.
DR PDBsum; 5GZ5; -.
DR PDBsum; 7CBA; -.
DR AlphaFoldDB; A0A2D0TC04; -.
DR SMR; A0A2D0TC04; -.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0043262; F:adenosine-diphosphatase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR Gene3D; 3.40.570.10; -; 1.
DR Gene3D; 3.40.720.10; -; 1.
DR InterPro; IPR017850; Alkaline_phosphatase_core_sf.
DR InterPro; IPR001604; DNA/RNA_non-sp_Endonuclease.
DR InterPro; IPR044929; DNA/RNA_non-sp_Endonuclease_sf.
DR InterPro; IPR020821; Extracellular_endonuc_su_A.
DR InterPro; IPR044925; His-Me_finger_sf.
DR InterPro; IPR002591; Phosphodiest/P_Trfase.
DR InterPro; IPR036024; Somatomedin_B-like_dom_sf.
DR InterPro; IPR001212; Somatomedin_B_dom.
DR Pfam; PF01223; Endonuclease_NS; 1.
DR Pfam; PF01663; Phosphodiest; 1.
DR Pfam; PF01033; Somatomedin_B; 2.
DR SMART; SM00892; Endonuclease_NS; 1.
DR SMART; SM00477; NUC; 1.
DR SMART; SM00201; SO; 2.
DR SUPFAM; SSF53649; SSF53649; 1.
DR SUPFAM; SSF54060; SSF54060; 1.
DR SUPFAM; SSF90188; SSF90188; 2.
DR PROSITE; PS00524; SMB_1; 2.
DR PROSITE; PS50958; SMB_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; Glycoprotein; Hemostasis impairing toxin;
KW Hydrolase; Metal-binding; Platelet aggregation inhibiting toxin; Repeat;
KW Secreted; Toxin.
FT CHAIN 1..830
FT /note="Venom phosphodiesterase"
FT /id="PRO_0000448282"
FT DOMAIN 7..50
FT /note="SMB 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT DOMAIN 51..95
FT /note="SMB 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT MOTIF 35..37
FT /note="Cell attachment site"
FT /evidence="ECO:0000255"
FT ACT_SITE 162
FT /note="AMP-threonine intermediate"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ5"
FT BINDING 124
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT BINDING 162
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT BINDING 248
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ5"
FT BINDING 282
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT BINDING 286
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT BINDING 286
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ5"
FT BINDING 329
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT BINDING 330
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT BINDING 439
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT CARBOHYD 16
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4"
FT CARBOHYD 193
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT CARBOHYD 236
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT CARBOHYD 247
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT CARBOHYD 489
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT CARBOHYD 723
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT CARBOHYD 742
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ5"
FT DISULFID 11..28
FT /note="Alternate"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4"
FT DISULFID 11..15
FT /note="Alternate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT DISULFID 15..46
FT /note="Alternate"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4"
FT DISULFID 26..39
FT /note="Alternate"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4"
FT DISULFID 26..28
FT /note="Alternate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT DISULFID 32..38
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4"
FT DISULFID 39..46
FT /note="Alternate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT DISULFID 55..72
FT /note="Alternate"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 55..60
FT /note="Alternate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT DISULFID 60..90
FT /note="Alternate"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 70..83
FT /note="Alternate"
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 70..72
FT /note="Alternate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT DISULFID 76..82
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 83..90
FT /note="Alternate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00350"
FT DISULFID 101..147
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 109..321
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 337..434
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 385..772
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 518..575
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 531..632
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 533..617
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT DISULFID 740..750
FT /evidence="ECO:0000269|Ref.1, ECO:0007744|PDB:5GZ4,
FT ECO:0007744|PDB:5GZ5"
FT HELIX 40..42
FT /evidence="ECO:0007829|PDB:5GZ4"
FT HELIX 43..47
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 74..80
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 86..90
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 118..123
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 128..134
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 139..147
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 148..152
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 162..171
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 175..178
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 182..187
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 188..191
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 196..199
FT /evidence="ECO:0007829|PDB:7CBA"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 204..206
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 212..218
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 223..227
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 229..232
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 235..237
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 241..243
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 248..250
FT /evidence="ECO:0007829|PDB:5GZ4"
FT HELIX 252..263
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 267..269
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 272..278
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 282..288
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 290..292
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 293..315
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 319..321
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 322..327
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 333..335
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 339..342
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 343..345
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 352..355
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 361..366
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 367..373
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 376..382
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 391..396
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 397..399
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 402..404
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 414..419
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 424..428
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 435..438
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 446..448
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 452..456
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 461..465
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 470..472
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 473..480
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 492..495
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 496..498
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 499..501
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 539..544
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 550..560
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 574..578
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 583..587
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 588..591
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 592..600
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 614..617
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 626..628
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 632..634
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 640..647
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 649..651
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 656..659
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 666..671
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 672..683
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 685..693
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 696..703
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 709..711
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 715..717
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 731..742
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 747..749
FT /evidence="ECO:0007829|PDB:5GZ4"
FT HELIX 752..754
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 755..763
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 769..771
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 782..787
FT /evidence="ECO:0007829|PDB:5GZ5"
FT STRAND 789..791
FT /evidence="ECO:0007829|PDB:7CBA"
FT HELIX 793..800
FT /evidence="ECO:0007829|PDB:5GZ5"
FT HELIX 812..820
FT /evidence="ECO:0007829|PDB:5GZ5"
FT TURN 826..828
FT /evidence="ECO:0007829|PDB:5GZ5"
SQ SEQUENCE 830 AA; 94616 MW; D3F4C1B1929E576E CRC64;
LKQSKQPLES CRNRCNETFS EELSYCSCDN KCTERKACCW DYQDICVLPT QSWSCNKLRC
GEKRMANVLC SCSEDCLTKK DCCTDYKSIC KRETSWLKDQ CASSSASQCP EGFDQSPLIL
FSMDGFRAEY LETWDTLMPN INKLKTCGTH AKYMRAVYPT KTFVNHYTIV TGLYAETHGI
IDNNMYDVKL NQNFSLSGSN MRNAAWWGGQ PIWHTASYQG LKAATYFWPG SEVKINGSYP
TIYKVYNKST PFEARVMEVL KWLDLPKAKR PDFSTLYIEE PDTTGHKFGP VSGQVIKSLQ
MADRTLGMLM EGLKQRNLHN CVNLILLADH GMEAISCNRL EYMTDYFNTV DFFMYEGAAP
RIRSKNVPKD FYTFDSEAIV KKLTCRKPKQ HFKAYLAKDL PKRLHFANNI RIDKVNLMVD
RQWLAVRNKK YKYCSGGTHG YDNEFKSMEA IFLAHGPGFK EKTEVTSFEN IEVYNLMCDL
LKLKPAPNNG THGSLNHLLK NPFYNPSPAK EQSPPLYCLF GPVPSPDVSG CKCSSITDLE
AVNQRLNLID QAKMQSEADN LPYGRPHVLQ HSKYCLLHQT KYISAYSQDI LMPLWNSYTI
SKSLVKPTSA PPSASDCLRL DVRIPTVQSQ TCSNYQPDLA ITPGFLYPPD FSSSGPEQYD
ALITSNIVPM YKEFARLWNY FHSTLLPKYA TERNGLNVIS GPIFDYNYDG HFDPYDTIDQ
YVNNTKIPIP THYFVVLTSC ENSTKTPLNC PPGSLKVLSF ILPHRPDNSE SCADKSPDNL
WVEERMQTHT ARVRDVELLT GLDFYSALKQ PLSETLRLKT FLPIFINSVN
