V5NTD_NAJAT
ID V5NTD_NAJAT Reviewed; 529 AA.
AC A0A2I4HXH5;
DT 16-OCT-2019, integrated into UniProtKB/Swiss-Prot.
DT 28-FEB-2018, sequence version 1.
DT 03-AUG-2022, entry version 12.
DE RecName: Full=Snake venom 5'-nucleotidase {ECO:0000303|Ref.1};
DE Short=5'-NT;
DE EC=3.1.3.5;
DE AltName: Full=Ecto-5'-nucleotidase;
DE Flags: Precursor; Fragment;
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:5H7W}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH ZINC, GLYCOSYLATION
RP AT ASN-308 AND ASN-322, AND DISULFIDE BOND.
RA Chang C., Lin C.-C., Wu W.-G.;
RT "Crystal strucuture of Taiwan cobra (Naja atra) venom 5'-nucleotidase at
RT 1.9 Angstroms resolution.";
RL Submitted (NOV-2016) to the PDB data bank.
RN [2]
RP REVIEW, AND FUNCTION.
RX PubMed=20186872; DOI=10.1002/cbf.1637;
RA Dhananjaya B.L., D'Souza C.J.;
RT "The pharmacological role of nucleotidases in snake venoms.";
RL Cell Biochem. Funct. 28:171-177(2010).
CC -!- FUNCTION: Hydrolyzes nucleotides into nucleosides (By similarity).
CC Snake venom 5'-nucleotidases are widely distributed among venomous
CC snake taxa, but there is a lack of information about their biological
CC activities. They have been shown to inhibit platelet aggregation. This
CC effect may be due to the liberation of inhibitory AMP or adenosine by
CC its action on ADP released upon initiation of aggregation. Venom 5'-
CC nucleotidases are also known to synergistically act in vivo with other
CC toxins like ADPases, phospholipases, and disintegrins to exert a more
CC pronounced anti-coagulant effect. {ECO:0000250|UniProtKB:P0DJJ5,
CC ECO:0000305|PubMed:20186872}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-phosphate + H2O = a ribonucleoside +
CC phosphate; Xref=Rhea:RHEA:12484, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:18254, ChEBI:CHEBI:43474, ChEBI:CHEBI:58043; EC=3.1.3.5;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250, ECO:0000305|Ref.1};
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000250|UniProtKB:P0DJJ5}; Lipid-
CC anchor, GPI-anchor {ECO:0000250|UniProtKB:P21589}.
CC -!- TISSUE SPECIFICITY: Expressed by the venom gland. {ECO:0000305|Ref.1}.
CC -!- PTM: Venom 5'-nucleotidases (or a part thereof) may be released into
CC the venom via exosome-like vesicles. They may be attached via a GPI
CC anchor to the membrane of these vesicles. Soluble forms of 5'-
CC nucleotidase might be released by cleavage of the ectodomain in the
CC exosome-like vesicles or venom gland cells.
CC -!- SIMILARITY: Belongs to the 5'-nucleotidase family. {ECO:0000305}.
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DR PDB; 5H7W; X-ray; 1.90 A; A/B=1-529.
DR PDB; 7D0V; X-ray; 2.17 A; A/B=1-529.
DR PDBsum; 5H7W; -.
DR PDBsum; 7D0V; -.
DR AlphaFoldDB; A0A2I4HXH5; -.
DR SMR; A0A2I4HXH5; -.
DR GO; GO:0031225; C:anchored component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0106411; F:XMP 5'-nucleosidase activity; IEA:UniProtKB-EC.
DR GO; GO:0009166; P:nucleotide catabolic process; IEA:InterPro.
DR Gene3D; 3.60.21.10; -; 1.
DR Gene3D; 3.90.780.10; -; 1.
DR InterPro; IPR008334; 5'-Nucleotdase_C.
DR InterPro; IPR036907; 5'-Nucleotdase_C_sf.
DR InterPro; IPR006146; 5'-Nucleotdase_CS.
DR InterPro; IPR006179; 5_nucleotidase/apyrase.
DR InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR PANTHER; PTHR11575; PTHR11575; 1.
DR Pfam; PF02872; 5_nucleotid_C; 1.
DR Pfam; PF00149; Metallophos; 1.
DR PRINTS; PR01607; APYRASEFAMLY.
DR SUPFAM; SSF55816; SSF55816; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
DR PROSITE; PS00785; 5_NUCLEOTIDASE_1; 1.
DR PROSITE; PS00786; 5_NUCLEOTIDASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; Glycoprotein; GPI-anchor; Hydrolase;
KW Lipoprotein; Membrane; Metal-binding; Nucleotide-binding; Signal; Zinc.
FT SIGNAL <1..1
FT /evidence="ECO:0000305"
FT CHAIN 2..>529
FT /note="Snake venom 5'-nucleotidase"
FT /evidence="ECO:0000250|UniProtKB:P0DJJ5"
FT /id="PRO_0000448287"
FT PROPEP 526..529
FT /note="Removed in mature form"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT /id="PRO_0000448288"
FT BINDING 12
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:5H7W"
FT BINDING 14
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:5H7W"
FT BINDING 60
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007744|PDB:5H7W"
FT BINDING 60
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:5H7W"
FT BINDING 92
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:5H7W"
FT BINDING 195
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:5H7W"
FT BINDING 218
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007744|PDB:5H7W"
FT BINDING 220
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT BINDING 329
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT BINDING 365
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT BINDING 370
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT BINDING 393
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT BINDING 476..482
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT SITE 93
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT SITE 96
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT LIPID 525
FT /note="GPI-anchor amidated serine"
FT /evidence="ECO:0000250|UniProtKB:P21589"
FT CARBOHYD 308
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0007744|PDB:5H7W"
FT CARBOHYD 322
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0007744|PDB:5H7W"
FT DISULFID 27..32
FT /evidence="ECO:0007744|PDB:5H7W"
FT DISULFID 328..333
FT /evidence="ECO:0007744|PDB:5H7W"
FT DISULFID 340..362
FT /evidence="ECO:0007744|PDB:5H7W"
FT DISULFID 452..455
FT /evidence="ECO:0007744|PDB:5H7W"
FT NON_TER 1
FT /evidence="ECO:0000305"
FT NON_TER 529
FT /evidence="ECO:0000305"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 36..49
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 51..57
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 62..65
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 66..71
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 74..82
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 92..95
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 98..103
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 106..109
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 119..121
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 123..125
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 126..132
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 133..141
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 144..152
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 156..159
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 166..168
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 171..184
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 190..196
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 198..207
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 213..215
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 225..227
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 229..231
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 238..243
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 249..253
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 260..270
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 275..280
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 293..310
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 315..319
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 325..328
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 334..346
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 362..365
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 366..368
FT /evidence="ECO:0007829|PDB:5H7W"
FT TURN 375..380
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 384..390
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 396..403
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 404..415
FT /evidence="ECO:0007829|PDB:5H7W"
FT TURN 416..419
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 426..435
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 445..451
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 453..457
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 459..462
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 467..474
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 475..478
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 481..483
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 485..487
FT /evidence="ECO:0007829|PDB:5H7W"
FT TURN 491..493
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 494..499
FT /evidence="ECO:0007829|PDB:5H7W"
FT HELIX 500..511
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 512..514
FT /evidence="ECO:0007829|PDB:5H7W"
FT STRAND 520..524
FT /evidence="ECO:0007829|PDB:5H7W"
SQ SEQUENCE 529 AA; 58198 MW; C149948EF728490D CRC64;
GSFELTILHT NDVHARLEQT SRDSGKCTGE DCYGGVARRA TKIRQIRASH RNVLLLDAGD
QYQGTIWFNY YKGREVVHFM NSLRYDAMAL GNHEFDNGLN GLLDPLLKNV KFPILSANIR
PKGPIASNIS GYILPYKIIN VGSEKVGIIG YTTKETPVLS NPGPYLEFRD EVEELQKHAD
KLTTLGVNKI IALGHSGFME DCRIAQKVKG VDVVVGGHTN TFLYTGSPPS NEVAAGNYPF
MQLSDDGRQV PVVQAYAFGK YLGYLNVTFD DKGKVIKASG NPILLNKSIQ EDPAVKAEIS
RMKVQLQNYS SQEIGRTIVY LNGTTHACRF HECNLGNLIC DAVVYNNLRH PDDNEWNHVS
MCIVNGGGIR SPIDEQANNG IITLEELTAV LPFGGTFDLL QIKGSTLRQA FEHSVHRHGQ
GTGELLQVSG IKVVYDLSQK PGKRVVSLNV LCTECRVPTY VPLEMEKTYK VLLPSFLAAG
GDGYYMLKGD SSNHSSGDLD ISIVGDYIKR MGKVFPAMEG RMVFSAGSL
