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Q5SH23

- LYSX_THET8

UniProt

Q5SH23 - LYSX_THET8

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Protein

Alpha-aminoadipate--LysW ligase LysX

Gene

lysX

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

Catalyzes the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.1 Publication

Catalytic activityi

ATP + [lysine-biosynthesis-protein LysW]-C-terminal-L-glutamate + L-2-aminoadipate = ADP + phosphate + [lysine-biosynthesis-protein LysW]-C-terminal-gamma-(L-2-aminoadip-2-yl)-L-glutamate.1 Publication

Cofactori

Mg2+By similarityNote: Binds 2 magnesium ions per subunit.By similarity

Kineticsi

  1. KM=2.1 mM for alpha-aminoadipate1 Publication
  2. KM=2.6 mM for ATP1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei89 – 891ATPBy similarity
Binding sitei129 – 1291ATP
Binding sitei194 – 1941ATP
Binding sitei202 – 2021ATPBy similarity
Metal bindingi237 – 2371Magnesium 1By similarity
Metal bindingi249 – 2491Magnesium 1By similarity
Metal bindingi249 – 2491Magnesium 2By similarity
Metal bindingi251 – 2511Magnesium 2By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi133 – 1397ATP
Nucleotide bindingi169 – 18012ATPAdd
BLAST

GO - Molecular functioni

  1. acid-amino acid ligase activity Source: UniProtKB-EC
  2. ATP binding Source: UniProtKB-KW
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cellular protein modification process Source: InterPro
  2. lysine biosynthetic process via aminoadipic acid Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-6728.
TTHE300852:GH8R-1953-MONOMER.
UniPathwayiUPA00033; UER00035.

Names & Taxonomyi

Protein namesi
Recommended name:
Alpha-aminoadipate--LysW ligase LysX (EC:6.3.2.431 Publication)
Short name:
AAA--LysW ligase LysX
Gene namesi
Name:lysX
Ordered Locus Names:TTHA1907
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000532: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 280280Alpha-aminoadipate--LysW ligase LysXPRO_0000391001Add
BLAST

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

STRINGi300852.TTHA1907.

Structurei

Secondary structure

1
280
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 87Combined sources
Helixi11 – 2212Combined sources
Beta strandi27 – 315Combined sources
Helixi32 – 343Combined sources
Helixi44 – 463Combined sources
Beta strandi51 – 544Combined sources
Helixi59 – 7113Combined sources
Beta strandi76 – 783Combined sources
Helixi80 – 878Combined sources
Helixi89 – 9911Combined sources
Beta strandi106 – 1116Combined sources
Helixi112 – 12211Combined sources
Beta strandi124 – 1296Combined sources
Beta strandi140 – 1423Combined sources
Helixi145 – 15814Combined sources
Helixi161 – 1644Combined sources
Beta strandi165 – 1706Combined sources
Beta strandi175 – 18410Combined sources
Beta strandi187 – 1959Combined sources
Beta strandi197 – 2004Combined sources
Helixi203 – 2053Combined sources
Beta strandi208 – 2114Combined sources
Helixi216 – 22813Combined sources
Beta strandi232 – 24110Combined sources
Beta strandi244 – 25310Combined sources
Helixi259 – 2635Combined sources
Helixi267 – 27711Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1UC8X-ray2.00A/B1-280[»]
1UC9X-ray2.38A/B1-280[»]
3VPDX-ray1.95A/B1-279[»]
ProteinModelPortaliQ5SH23.
SMRiQ5SH23. Positions 1-280.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SH23.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 276184ATP-graspPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi258 – 2592N-[TS] motif that is essential for LysX substrate specificity

Sequence similaritiesi

Belongs to the RimK family. LysX subfamily.Curated
Contains 1 ATP-grasp domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0189.
HOGENOMiHOG000228553.
KOiK05827.
OMAiACMERIA.
OrthoDBiEOG6DZDX8.
PhylomeDBiQ5SH23.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
InterProiIPR011761. ATP-grasp.
IPR013651. ATP-grasp_RimK-type.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR011870. LysX_arch.
IPR016185. PreATP-grasp_dom.
IPR004666. RpS6_RimK/Lys_biosynth_LsyX.
[Graphical view]
PfamiPF08443. RimK. 1 hit.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR02144. LysX_arch. 1 hit.
TIGR00768. rimK_fam. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5SH23-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLAILYDRIR PDERMLFERA EALGLPYKKV YVPALPMVLG ERPKELEGVT
60 70 80 90 100
VALERCVSQS RGLAAARYLT ALGIPVVNRP EVIEACGDKW ATSVALAKAG
110 120 130 140 150
LPQPKTALAT DREEALRLME AFGYPVVLKP VIGSWGRLLA KVTDRAAAEA
160 170 180 190 200
LLEHKEVLGG FQHQLFYIQE YVEKPGRDIR VFVVGERAIA AIYRRSAHWI
210 220 230 240 250
TNTARGGQAE NCPLTEEVAR LSVKAAEAVG GGVVAVDLFE SERGLLVNEV
260 270 280
NHTMEFKNSV HTTGVDIPGE ILKYAWSLAS
Length:280
Mass (Da):30,718
Last modified:December 21, 2004 - v1
Checksum:iB168629146AF1344
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB103032 Genomic DNA. Translation: BAC67243.1.
AP008226 Genomic DNA. Translation: BAD71730.1.
RefSeqiWP_011229004.1. NC_006461.1.
YP_145173.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD71730; BAD71730; BAD71730.
GeneIDi3167971.
KEGGittj:TTHA1907.
PATRICi23958779. VBITheThe93045_1875.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB103032 Genomic DNA. Translation: BAC67243.1 .
AP008226 Genomic DNA. Translation: BAD71730.1 .
RefSeqi WP_011229004.1. NC_006461.1.
YP_145173.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1UC8 X-ray 2.00 A/B 1-280 [» ]
1UC9 X-ray 2.38 A/B 1-280 [» ]
3VPD X-ray 1.95 A/B 1-279 [» ]
ProteinModelPortali Q5SH23.
SMRi Q5SH23. Positions 1-280.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 300852.TTHA1907.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD71730 ; BAD71730 ; BAD71730 .
GeneIDi 3167971.
KEGGi ttj:TTHA1907.
PATRICi 23958779. VBITheThe93045_1875.

Phylogenomic databases

eggNOGi COG0189.
HOGENOMi HOG000228553.
KOi K05827.
OMAi ACMERIA.
OrthoDBi EOG6DZDX8.
PhylomeDBi Q5SH23.

Enzyme and pathway databases

UniPathwayi UPA00033 ; UER00035 .
BioCyci MetaCyc:MONOMER-6728.
TTHE300852:GH8R-1953-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q5SH23.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
InterProi IPR011761. ATP-grasp.
IPR013651. ATP-grasp_RimK-type.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR011870. LysX_arch.
IPR016185. PreATP-grasp_dom.
IPR004666. RpS6_RimK/Lys_biosynth_LsyX.
[Graphical view ]
Pfami PF08443. RimK. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR02144. LysX_arch. 1 hit.
TIGR00768. rimK_fam. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Crystal structure of a lysine biosynthesis enzyme, LysX, from Thermus thermophilus HB8."
    Sakai H., Vassylyeva M.N., Matsuura T., Sekine S., Gotoh K., Nishiyama M., Terada T., Shirouzu M., Kuramitsu S., Vassylyev D.G., Yokoyama S.
    J. Mol. Biol. 332:729-740(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH ADP, SUBUNIT.
    Strain: HB8 / ATCC 27634 / DSM 579.
  2. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  3. "Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus."
    Horie A., Tomita T., Saiki A., Kono H., Taka H., Mineki R., Fujimura T., Nishiyama C., Kuzuyama T., Nishiyama M.
    Nat. Chem. Biol. 5:673-679(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
  4. Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH ATP ANALOG.

Entry informationi

Entry nameiLYSX_THET8
AccessioniPrimary (citable) accession number: Q5SH23
Secondary accession number(s): Q84BR0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 19, 2010
Last sequence update: December 21, 2004
Last modified: November 26, 2014
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3