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Q5SH23

- LYSX_THET8

UniProt

Q5SH23 - LYSX_THET8

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Protein

Alpha-aminoadipate--LysW ligase LysX

Gene
lysX, TTHA1907
Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Status
Reviewed - Annotation score: 5 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 + [LysW] + L-2-aminoadipate = ADP + phosphate + [LysW]-L-2-aminoadipate.1 Publication

Cofactori

Binds 2 magnesium ions per subunit By similarity.

Kineticsi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei89 – 891ATP By similarity
Binding sitei129 – 1291ATP
Binding sitei194 – 1941ATP
Binding sitei202 – 2021ATP By similarity
Metal bindingi237 – 2371Magnesium 1 By similarity
Metal bindingi249 – 2491Magnesium 1 By similarity
Metal bindingi249 – 2491Magnesium 2 By similarity
Metal bindingi251 – 2511Magnesium 2 By 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.n4)
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.1 Publication

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 – 87
Helixi11 – 2212
Beta strandi27 – 315
Helixi32 – 343
Helixi44 – 463
Beta strandi51 – 544
Helixi59 – 7113
Beta strandi76 – 783
Helixi80 – 878
Helixi89 – 9911
Beta strandi106 – 1116
Helixi112 – 12211
Beta strandi124 – 1296
Beta strandi140 – 1423
Helixi145 – 15814
Helixi161 – 1644
Beta strandi165 – 1706
Beta strandi175 – 18410
Beta strandi187 – 1959
Beta strandi197 – 2004
Helixi203 – 2053
Beta strandi208 – 2114
Helixi216 – 22813
Beta strandi232 – 24110
Beta strandi244 – 25310
Helixi259 – 2635
Helixi267 – 27711

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiQ5SH23.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini93 – 276184ATP-graspAdd
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.
Contains 1 ATP-grasp domain.

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

MLAILYDRIR PDERMLFERA EALGLPYKKV YVPALPMVLG ERPKELEGVT    50
VALERCVSQS RGLAAARYLT ALGIPVVNRP EVIEACGDKW ATSVALAKAG 100
LPQPKTALAT DREEALRLME AFGYPVVLKP VIGSWGRLLA KVTDRAAAEA 150
LLEHKEVLGG FQHQLFYIQE YVEKPGRDIR VFVVGERAIA AIYRRSAHWI 200
TNTARGGQAE NCPLTEEVAR LSVKAAEAVG GGVVAVDLFE SERGLLVNEV 250
NHTMEFKNSV HTTGVDIPGE ILKYAWSLAS 280
Length:280
Mass (Da):30,718
Last modified:December 21, 2004 - v1
Checksum:iB168629146AF1344
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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:
PDBe
RCSB PDB
PDBj
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: September 3, 2014
This is version 70 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

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