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Glutamine-dependent NAD( ) synthetase (EC 6.3.5.1) (NAD( ) synthase [glutamine-hydrolyzing])

 NADE_MYCTU              Reviewed;         679 AA.
P9WJJ3; L0T9M3; P0A5L6; P71911;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
25-OCT-2017, entry version 25.
RecName: Full=Glutamine-dependent NAD(+) synthetase {ECO:0000255|HAMAP-Rule:MF_02090, ECO:0000303|PubMed:19270703, ECO:0000303|PubMed:22280445};
EC=6.3.5.1 {ECO:0000255|HAMAP-Rule:MF_02090, ECO:0000269|PubMed:15748981, ECO:0000269|PubMed:19270703, ECO:0000269|PubMed:9620974};
AltName: Full=NAD(+) synthase [glutamine-hydrolyzing] {ECO:0000255|HAMAP-Rule:MF_02090};
Name=nadE {ECO:0000255|HAMAP-Rule:MF_02090};
OrderedLocusNames=Rv2438c; ORFNames=MTCY428.08;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=9620974;
Cantoni R., Branzoni M., Labo M., Rizzi M., Riccardi G.;
"The MTCY428.08 gene of Mycobacterium tuberculosis codes for NAD+
synthetase.";
J. Bacteriol. 180:3218-3221(1998).
[3]
FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF GLU-52; LYS-121 AND
CYS-176, AND ACTIVE SITE.
PubMed=15748981; DOI=10.1016/j.resmic.2004.08.011;
Bellinzoni M., Buroni S., Pasca M.R., Guglierame P., Arcesi F.,
De Rossi E., Riccardi G.;
"Glutamine amidotransferase activity of NAD+ synthetase from
Mycobacterium tuberculosis depends on an amino-terminal nitrilase
domain.";
Res. Microbiol. 156:173-177(2005).
[4]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[5] {ECO:0000244|PDB:3DLA}
X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH DEAMIDO-NAD,
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY,
SUBUNIT, DOMAIN, ACTIVE SITE, AND MUTAGENESIS OF ASP-656.
PubMed=19270703; DOI=10.1038/nsmb.1567;
LaRonde-LeBlanc N., Resto M., Gerratana B.;
"Regulation of active site coupling in glutamine-dependent NAD(+)
synthetase.";
Nat. Struct. Mol. Biol. 16:421-429(2009).
[6] {ECO:0000244|PDB:3SDB, ECO:0000244|PDB:3SEQ, ECO:0000244|PDB:3SEZ, ECO:0000244|PDB:3SYT, ECO:0000244|PDB:3SZG}
X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH AMP; ATP;
L-GLUTAMIC ACID; NAD; DEAMIDO-NAD AND DIPHOSPHATE, ENZYME REGULATION,
SUBUNIT, AND DOMAIN.
PubMed=22280445; DOI=10.1042/BJ20112210;
Chuenchor W., Doukov T.I., Resto M., Chang A., Gerratana B.;
"Regulation of the intersubunit ammonia tunnel in Mycobacterium
tuberculosis glutamine-dependent NAD+ synthetase.";
Biochem. J. 443:417-426(2012).
-!- FUNCTION: Catalyzes the ATP-dependent amidation of deamido-NAD to
form NAD. Uses L-glutamine as a nitrogen source. In vitro, can
also use ammonia with comparable specific activity.
{ECO:0000269|PubMed:15748981, ECO:0000269|PubMed:19270703,
ECO:0000269|PubMed:9620974}.
-!- CATALYTIC ACTIVITY: ATP + deamido-NAD(+) + L-glutamine + H(2)O =
AMP + diphosphate + NAD(+) + L-glutamate. {ECO:0000255|HAMAP-
Rule:MF_02090, ECO:0000269|PubMed:15748981,
ECO:0000269|PubMed:19270703, ECO:0000269|PubMed:9620974}.
-!- ENZYME REGULATION: The formation of the intermediates complex at
the synthetase domain stimulates the glutaminase activity.
{ECO:0000269|PubMed:22280445}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.3 mM for glutamine {ECO:0000269|PubMed:19270703};
KM=0.13 mM for deamido-NAD(+) (with glutamine as a nitrogen
source) {ECO:0000269|PubMed:19270703};
KM=0.12 mM for ATP (with glutamine as a nitrogen source)
{ECO:0000269|PubMed:19270703};
KM=20 mM for ammonia {ECO:0000269|PubMed:19270703};
KM=0.7 mM for deamido-NAD(+) (with ammonia as a nitrogen source)
{ECO:0000269|PubMed:19270703};
KM=1.4 mM for ATP (with ammonia as a nitrogen source)
{ECO:0000269|PubMed:19270703};
Note=kcat is 0.55 sec(-1) for glutamine-dependent activity. kcat
is 2.8 sec(-1) for ammonia-dependent activity.
{ECO:0000269|PubMed:19270703};
-!- PATHWAY: Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from
deamido-NAD(+) (L-Gln route): step 1/1. {ECO:0000255|HAMAP-
Rule:MF_02090, ECO:0000305|PubMed:19270703}.
-!- SUBUNIT: Homooctamer; composed of two stacked homotetramers that
form a ring-like structure. {ECO:0000269|PubMed:19270703,
ECO:0000269|PubMed:22280445}.
-!- INTERACTION:
Self; NbExp=2; IntAct=EBI-15763158, EBI-15763158;
-!- DOMAIN: An ammonia tunnel 40 Angstroms long allows transfer of
ammonia from the glutaminase active site, where it is produced, to
the synthetase active site, where it is used for the ATP-dependent
formation of NAD(+). {ECO:0000269|PubMed:19270703,
ECO:0000269|PubMed:22280445}.
-!- SIMILARITY: In the C-terminal section; belongs to the NAD
synthetase family. {ECO:0000255|HAMAP-Rule:MF_02090, ECO:0000305}.
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EMBL; AL123456; CCP45230.1; -; Genomic_DNA.
PIR; D70680; D70680.
RefSeq; NP_216954.2; NC_000962.3.
RefSeq; WP_003901403.1; NZ_KK339370.1.
PDB; 3DLA; X-ray; 2.35 A; A/B/C/D=1-679.
PDB; 3SDB; X-ray; 2.00 A; A=1-679.
PDB; 3SEQ; X-ray; 2.73 A; A/B/C/D=1-679.
PDB; 3SEZ; X-ray; 2.65 A; A/B/C/D=1-679.
PDB; 3SYT; X-ray; 2.65 A; A/B/C/D=1-679.
PDB; 3SZG; X-ray; 2.25 A; A/B/C/D=1-679.
PDBsum; 3DLA; -.
PDBsum; 3SDB; -.
PDBsum; 3SEQ; -.
PDBsum; 3SEZ; -.
PDBsum; 3SYT; -.
PDBsum; 3SZG; -.
ProteinModelPortal; P9WJJ3; -.
SMR; P9WJJ3; -.
STRING; 83332.Rv2438c; -.
PaxDb; P9WJJ3; -.
EnsemblBacteria; CCP45230; CCP45230; Rv2438c.
GeneID; 885808; -.
KEGG; mtu:Rv2438c; -.
TubercuList; Rv2438c; -.
eggNOG; ENOG4108DWA; Bacteria.
eggNOG; COG0171; LUCA.
eggNOG; COG0388; LUCA.
KO; K01950; -.
OMA; RLAQDCY; -.
PhylomeDB; P9WJJ3; -.
BRENDA; 6.3.5.1; 3445.
UniPathway; UPA00253; UER00334.
Proteomes; UP000001584; Chromosome.
GO; GO:0005618; C:cell wall; IDA:MTBBASE.
GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
GO; GO:0005886; C:plasma membrane; IDA:MTBBASE.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0016810; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds; IEA:InterPro.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0003952; F:NAD+ synthase (glutamine-hydrolyzing) activity; IDA:MTBBASE.
GO; GO:0008795; F:NAD+ synthase activity; IBA:GO_Central.
GO; GO:0040007; P:growth; IMP:MTBBASE.
GO; GO:0009435; P:NAD biosynthetic process; IDA:MTBBASE.
CDD; cd00553; NAD_synthase; 1.
Gene3D; 3.40.50.620; -; 1.
Gene3D; 3.60.110.10; -; 1.
HAMAP; MF_02090; NadE_glutamine_dep; 1.
InterPro; IPR003010; C-N_Hydrolase.
InterPro; IPR036526; C-N_Hydrolase_sf.
InterPro; IPR014445; Gln-dep_NAD_synthase.
InterPro; IPR022310; NAD/GMP_synthase.
InterPro; IPR003694; NAD_synthase.
InterPro; IPR014729; Rossmann-like_a/b/a_fold.
PANTHER; PTHR23090; PTHR23090; 1.
Pfam; PF00795; CN_hydrolase; 1.
Pfam; PF02540; NAD_synthase; 1.
PIRSF; PIRSF006630; NADS_GAT; 1.
SUPFAM; SSF56317; SSF56317; 1.
PROSITE; PS50263; CN_HYDROLASE; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Ligase; NAD;
Nucleotide-binding; Reference proteome.
CHAIN 1 679 Glutamine-dependent NAD(+) synthetase.
/FTId=PRO_0000152241.
DOMAIN 12 276 CN hydrolase. {ECO:0000255|PROSITE-
ProRule:PRU00054}.
NP_BIND 366 373 ATP. {ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG, ECO:0000255|HAMAP-
Rule:MF_02090}.
NP_BIND 490 493 Deamido-NAD. {ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG, ECO:0000255|HAMAP-
Rule:MF_02090}.
REGION 337 679 Ligase.
ACT_SITE 52 52 Proton acceptor; for glutaminase
activity. {ECO:0000255|HAMAP-
Rule:MF_02090,
ECO:0000305|PubMed:15748981,
ECO:0000305|PubMed:19270703}.
ACT_SITE 121 121 For glutaminase activity.
{ECO:0000255|HAMAP-Rule:MF_02090,
ECO:0000305|PubMed:15748981,
ECO:0000305|PubMed:19270703}.
ACT_SITE 176 176 Nucleophile; for glutaminase activity.
{ECO:0000255|HAMAP-Rule:MF_02090,
ECO:0000305|PubMed:15748981,
ECO:0000305|PubMed:19270703}.
BINDING 127 127 L-glutamine. {ECO:0000244|PDB:3SYT,
ECO:0000255|HAMAP-Rule:MF_02090}.
BINDING 203 203 L-glutamine. {ECO:0000244|PDB:3SYT,
ECO:0000255|HAMAP-Rule:MF_02090}.
BINDING 209 209 L-glutamine. {ECO:0000244|PDB:3SYT,
ECO:0000255|HAMAP-Rule:MF_02090}.
BINDING 354 354 Deamido-NAD; shared with neighboring
subunit. {ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG}.
BINDING 456 456 Deamido-NAD. {ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SZG, ECO:0000255|HAMAP-
Rule:MF_02090}.
BINDING 471 471 Deamido-NAD; shared with neighboring
subunit. {ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG}.
BINDING 475 475 Deamido-NAD; via carbonyl oxygen; shared
with neighboring subunit.
{ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG}.
BINDING 480 480 ATP. {ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG, ECO:0000255|HAMAP-
Rule:MF_02090}.
BINDING 485 485 Deamido-NAD. {ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT, ECO:0000255|HAMAP-
Rule:MF_02090}.
BINDING 501 501 Deamido-NAD; shared with neighboring
subunit. {ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG}.
BINDING 635 635 Deamido-NAD. {ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SEQ,
ECO:0000244|PDB:3SEZ,
ECO:0000244|PDB:3SYT,
ECO:0000244|PDB:3SZG, ECO:0000255|HAMAP-
Rule:MF_02090}.
BINDING 661 661 Deamido-NAD; via carbonyl oxygen.
{ECO:0000244|PDB:3DLA,
ECO:0000244|PDB:3SZG}.
MUTAGEN 52 52 E->A: Lack of glutamine-dependent
activity. Retains 30% of ammonia-
dependent activity.
{ECO:0000269|PubMed:15748981}.
MUTAGEN 121 121 K->A: Lack of glutamine-dependent and
ammonia-dependent activities.
{ECO:0000269|PubMed:15748981}.
MUTAGEN 176 176 C->A: Lack of glutamine-dependent
activity. Retains 90% of ammonia-
dependent activity.
{ECO:0000269|PubMed:15748981}.
MUTAGEN 656 656 D->A: Causes a decrease in ammonia
channel efficiency to 70% compared with
wild-type enzyme.
{ECO:0000269|PubMed:19270703}.
HELIX 7 9 {ECO:0000244|PDB:3SDB}.
STRAND 11 18 {ECO:0000244|PDB:3SDB}.
HELIX 26 42 {ECO:0000244|PDB:3SDB}.
STRAND 46 49 {ECO:0000244|PDB:3SDB}.
TURN 52 56 {ECO:0000244|PDB:3SDB}.
HELIX 58 65 {ECO:0000244|PDB:3SDB}.
HELIX 67 84 {ECO:0000244|PDB:3SDB}.
STRAND 88 99 {ECO:0000244|PDB:3SDB}.
STRAND 102 111 {ECO:0000244|PDB:3SDB}.
STRAND 114 120 {ECO:0000244|PDB:3SDB}.
HELIX 132 134 {ECO:0000244|PDB:3SDB}.
STRAND 144 148 {ECO:0000244|PDB:3SDB}.
STRAND 151 157 {ECO:0000244|PDB:3SDB}.
STRAND 159 163 {ECO:0000244|PDB:3SDB}.
STRAND 170 175 {ECO:0000244|PDB:3SDB}.
HELIX 176 180 {ECO:0000244|PDB:3SDB}.
STRAND 181 183 {ECO:0000244|PDB:3SDB}.
HELIX 185 192 {ECO:0000244|PDB:3SDB}.
STRAND 196 200 {ECO:0000244|PDB:3SDB}.
HELIX 209 223 {ECO:0000244|PDB:3SDB}.
STRAND 226 231 {ECO:0000244|PDB:3SDB}.
STRAND 248 252 {ECO:0000244|PDB:3SDB}.
STRAND 255 259 {ECO:0000244|PDB:3SDB}.
STRAND 268 275 {ECO:0000244|PDB:3SDB}.
HELIX 276 285 {ECO:0000244|PDB:3SDB}.
HELIX 287 295 {ECO:0000244|PDB:3SDB}.
HELIX 297 301 {ECO:0000244|PDB:3SDB}.
STRAND 304 308 {ECO:0000244|PDB:3SDB}.
HELIX 333 357 {ECO:0000244|PDB:3SDB}.
STRAND 362 366 {ECO:0000244|PDB:3SDB}.
HELIX 371 386 {ECO:0000244|PDB:3SDB}.
HELIX 391 393 {ECO:0000244|PDB:3SDB}.
STRAND 394 398 {ECO:0000244|PDB:3SDB}.
HELIX 411 419 {ECO:0000244|PDB:3SDB}.
STRAND 422 425 {ECO:0000244|PDB:3SDB}.
HELIX 429 438 {ECO:0000244|PDB:3SDB}.
HELIX 442 445 {ECO:0000244|PDB:3SZG}.
HELIX 453 473 {ECO:0000244|PDB:3SDB}.
STRAND 475 479 {ECO:0000244|PDB:3SDB}.
HELIX 483 488 {ECO:0000244|PDB:3SDB}.
STRAND 494 496 {ECO:0000244|PDB:3SDB}.
STRAND 501 503 {ECO:0000244|PDB:3SDB}.
TURN 504 507 {ECO:0000244|PDB:3SDB}.
HELIX 510 523 {ECO:0000244|PDB:3SDB}.
TURN 524 526 {ECO:0000244|PDB:3SEQ}.
HELIX 528 542 {ECO:0000244|PDB:3SDB}.
HELIX 558 561 {ECO:0000244|PDB:3SDB}.
HELIX 564 577 {ECO:0000244|PDB:3SDB}.
HELIX 581 592 {ECO:0000244|PDB:3SDB}.
STRAND 595 598 {ECO:0000244|PDB:3SYT}.
HELIX 606 608 {ECO:0000244|PDB:3SDB}.
HELIX 614 629 {ECO:0000244|PDB:3SDB}.
HELIX 633 636 {ECO:0000244|PDB:3SDB}.
TURN 653 656 {ECO:0000244|PDB:3SDB}.
HELIX 666 675 {ECO:0000244|PDB:3SDB}.
SEQUENCE 679 AA; 74683 MW; 14AC29CE434A8B0D CRC64;
MNFYSAYQHG FVRVAACTHH TTIGDPAANA ASVLDMARAC HDDGAALAVF PELTLSGYSI
EDVLLQDSLL DAVEDALLDL VTESADLLPV LVVGAPLRHR HRIYNTAVVI HRGAVLGVVP
KSYLPTYREF YERRQMAPGD GERGTIRIGG ADVAFGTDLL FAASDLPGFV LHVEICEDMF
VPMPPSAEAA LAGATVLANL SGSPITIGRA EDRRLLARSA SARCLAAYVY AAAGEGESTT
DLAWDGQTMI WENGALLAES ERFPKGVRRS VADVDTELLR SERLRMGTFD DNRRHHRELT
ESFRRIDFAL DPPAGDIGLL REVERFPFVP ADPQRLQQDC YEAYNIQVSG LEQRLRALDY
PKVVIGVSGG LDSTHALIVA THAMDREGRP RSDILAFALP GFATGEHTKN NAIKLARALG
VTFSEIDIGD TARLMLHTIG HPYSVGEKVY DVTFENVQAG LRTDYLFRIA NQRGGIVLGT
GDLSELALGW STYGVGDQMS HYNVNAGVPK TLIQHLIRWV ISAGEFGEKV GEVLQSVLDT
EITPELIPTG EEELQSSEAK VGPFALQDFS LFQVLRYGFR PSKIAFLAWH AWNDAERGNW
PPGFPKSERP SYSLAEIRHW LQIFVQRFYS FSQFKRSALP NGPKVSHGGA LSPRGDWRAP
SDMSARIWLD QIDREVPKG


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6017 Snell Ave, Ste 357
San Jose, CA 95123




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