PURZ_BPVC8
ID PURZ_BPVC8 Reviewed; 343 AA.
AC G3FFN6;
DT 29-SEP-2021, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=N6-succino-2-amino-2'-deoxyadenylate synthase {ECO:0000255|HAMAP-Rule:MF_04166, ECO:0000303|PubMed:33926955};
DE AltName: Full=PurZ {ECO:0000255|HAMAP-Rule:MF_04166};
GN Name=purZ {ECO:0000255|HAMAP-Rule:MF_04166};
GN ORFNames=phiVC8_p27 {ECO:0000312|EMBL:AEM62924.1};
OS Vibrio phage phiVC8.
OC Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes;
OC Caudovirales; Podoviridae; Enhodamvirus.
OX NCBI_TaxID=1076759;
OH NCBI_TaxID=666; Vibrio cholerae.
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=27000701; DOI=10.1186/s12985-016-0490-x;
RA Solis-Sanchez A., Hernandez-Chinas U., Navarro-Ocana A., De la Mora J.,
RA Xicohtencatl-Cortes J., Eslava-Campos C.;
RT "Genetic characterization of OVC8 lytic phage for Vibrio cholerae O1.";
RL Virol. J. 13:47-47(2016).
RN [2]
RP BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, ACTIVE SITE, FUNCTION,
RP AND PATHWAY.
RX PubMed=33926954; DOI=10.1126/science.abe4882;
RA Zhou Y., Xu X., Wei Y., Cheng Y., Guo Y., Khudyakov I., Liu F., He P.,
RA Song Z., Li Z., Gao Y., Ang E.L., Zhao H., Zhang Y., Zhao S.;
RT "A widespread pathway for substitution of adenine by diaminopurine in phage
RT genomes.";
RL Science 372:512-516(2021).
RN [3] {ECO:0007744|PDB:6FLF, ECO:0007744|PDB:6FM0, ECO:0007744|PDB:6FM1, ECO:0007744|PDB:6TNH}
RP X-RAY CRYSTALLOGRAPHY (1.33 ANGSTROMS) OF 3-343 IN COMPLEX WITH ATP; DGMP
RP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=33926955; DOI=10.1126/science.abe6494;
RA Sleiman D., Garcia P.S., Lagune M., Loc'h J., Haouz A., Taib N.,
RA Roethlisberger P., Gribaldo S., Marliere P., Kaminski P.A.;
RT "A third purine biosynthetic pathway encoded by aminoadenine-based viral
RT DNA genomes.";
RL Science 372:516-520(2021).
CC -!- FUNCTION: Involved in the synthesis of the atypical nucleotide dZTP (2-
CC amino-2'-deoxyadenosine-5'-triphosphate) (PubMed:33926954). Involved in
CC the synthesis of N6-succino-2-amino-2'-deoxyadenylate, which undergoes
CC defumarylation and phosphorylation respectively by host PurB and
CC guanylate/nucleoside diphosphate kinases to give dZTP (2-amino-2'-
CC deoxyadenosine-5'-triphosphate) (PubMed:33926955). dZTP is integrated
CC into the viral genome instead of adenine by the viral polymerase. This
CC Z-base probably completely replaces adenosine and forms a triple bond
CC to the opposite T-base (PubMed:33926955). The resulting non-standard
CC viral DNA is called Z-genome (PubMed:33926955). The chemically modified
CC DNA is probably harder for the host bacteria to digest with nucleases
CC or restriction enzymes (Probable). {ECO:0000255|HAMAP-Rule:MF_04166,
CC ECO:0000269|PubMed:33926954, ECO:0000269|PubMed:33926955}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + dGMP + L-aspartate = (2S)-2-amino-2'-deoxyadenylo-
CC succinate + ADP + 2 H(+) + phosphate; Xref=Rhea:RHEA:67628,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29991, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57673, ChEBI:CHEBI:172924,
CC ChEBI:CHEBI:456216; Evidence={ECO:0000255|HAMAP-Rule:MF_04166,
CC ECO:0000269|PubMed:33926954};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_04166,
CC ECO:0000269|PubMed:33926955};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.8 uM for dGMP {ECO:0000269|PubMed:33926954};
CC KM=13 uM for dGMP {ECO:0000269|PubMed:33926955};
CC KM=4.1 uM for ATP {ECO:0000269|PubMed:33926954};
CC KM=90 uM for ATP {ECO:0000269|PubMed:33926955};
CC KM=80.5 uM for Asp {ECO:0000269|PubMed:33926954};
CC KM=2900 uM for Asp {ECO:0000269|PubMed:33926955};
CC -!- PATHWAY: Purine metabolism. {ECO:0000255|HAMAP-Rule:MF_04166,
CC ECO:0000269|PubMed:33926954}.
CC -!- SIMILARITY: Belongs to the Caudovirales PurZ family.
CC {ECO:0000255|HAMAP-Rule:MF_04166}.
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DR EMBL; JF712866; AEM62924.1; -; Genomic_DNA.
DR RefSeq; YP_009140156.1; NC_027118.1.
DR PDB; 6FKO; X-ray; 2.10 A; A/B=3-343.
DR PDB; 6FLF; X-ray; 1.33 A; A=3-343.
DR PDB; 6FM0; X-ray; 1.70 A; A/B=3-343.
DR PDB; 6FM1; X-ray; 2.35 A; A/B=1-343.
DR PDB; 6FM3; X-ray; 1.95 A; A=3-343.
DR PDB; 6RM2; X-ray; 2.50 A; A/B=1-343.
DR PDB; 6TNH; X-ray; 2.21 A; A/B=3-343.
DR PDBsum; 6FKO; -.
DR PDBsum; 6FLF; -.
DR PDBsum; 6FM0; -.
DR PDBsum; 6FM1; -.
DR PDBsum; 6FM3; -.
DR PDBsum; 6RM2; -.
DR PDBsum; 6TNH; -.
DR SMR; G3FFN6; -.
DR GeneID; 24366411; -.
DR KEGG; vg:24366411; -.
DR BRENDA; 6.3.4.25; 17967.
DR Proteomes; UP000008906; Genome.
DR GO; GO:0004019; F:adenylosuccinate synthase activity; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0005525; F:GTP binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006164; P:purine nucleotide biosynthetic process; IDA:UniProtKB.
DR Gene3D; 3.40.440.10; -; 2.
DR HAMAP; MF_00011; Adenylosucc_synth; 1.
DR HAMAP; MF_04166; Phage_PURZ; 1.
DR InterPro; IPR042109; Adenylosuccinate_synth_dom1.
DR InterPro; IPR001114; Adenylosuccinate_synthetase.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR046383; Phage_PurZ.
DR PANTHER; PTHR11846; PTHR11846; 2.
DR Pfam; PF00709; Adenylsucc_synt; 2.
DR SMART; SM00788; Adenylsucc_synt; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Magnesium; Metal-binding; Nucleotide-binding;
KW Purine biosynthesis; Reference proteome.
FT CHAIN 1..343
FT /note="N6-succino-2-amino-2'-deoxyadenylate synthase"
FT /id="PRO_0000453680"
FT ACT_SITE 14
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04166,
FT ECO:0000305|PubMed:33926954"
FT BINDING 14
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04166,
FT ECO:0000305|PubMed:33926954, ECO:0000305|PubMed:33926955"
FT BINDING 34..39
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:33926955"
FT BINDING 42
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04166,
FT ECO:0000305|PubMed:33926955"
FT BINDING 262
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04166,
FT ECO:0000269|PubMed:33926955"
FT BINDING 263
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04166,
FT ECO:0000305|PubMed:33926955"
FT BINDING 264
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04166,
FT ECO:0000269|PubMed:33926955"
FT BINDING 269
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_04166,
FT ECO:0000269|PubMed:33926955"
FT BINDING 294..297
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:33926954"
FT STRAND 4..13
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 17..28
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 31..35
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 43..46
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 60..63
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 80..89
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 91..94
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 99..102
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 111..117
FT /evidence="ECO:0007829|PDB:6FKO"
FT HELIX 119..124
FT /evidence="ECO:0007829|PDB:6FKO"
FT HELIX 132..141
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 151..154
FT /evidence="ECO:0007829|PDB:6FLF"
FT TURN 155..157
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 159..162
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 168..177
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 179..184
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:6FLF"
FT TURN 196..199
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 208..215
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 219..221
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 222..232
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:6FKO"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:6FKO"
FT TURN 263..265
FT /evidence="ECO:0007829|PDB:6FKO"
FT STRAND 270..272
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 276..286
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 289..294
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 296..298
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 301..317
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 323..328
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 330..332
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 333..335
FT /evidence="ECO:0007829|PDB:6FLF"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:6FLF"
FT HELIX 339..342
FT /evidence="ECO:0007829|PDB:6FLF"
SQ SEQUENCE 343 AA; 38183 MW; FA811BE8FDABD7A4 CRC64;
MKNVDLVIDL QFGSTGKGLI AGYLAEKNGY DTVINANMPN AGHTYINAEG RKWMHKVLPN
GIVSPNLKRV MLGAGSVFSI NRLMEEIEMS KDLLHDKVAI LIHPMATVLD EEAHKKAEVG
IATSIGSTGQ GSMAAMVEKL QRDPTNNTIV ARDVAQYDGR IAQYVCTVEE WDMALMASER
ILAEGAQGFS LSLNQEFYPY CTSRDCTPAR FLADMGIPLP MLNKVIGTAR CHPIRVGGTS
GGHYPDQEEL TWEQLGQVPE LTTVTKKVRR VFSFSFIQMQ KAMWTCQPDE VFLNFCNYLS
PMGWQDIVHQ IEVAAQSRYC DAEVKYLGFG PTFNDVELRE DVM
