Q5SH23 (LYSX_THET8) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Alpha-aminoadipate--LysW ligase LysX
Short name=AAA--LysW ligase LysX
EC=6.3.2.n4

Gene names

Name:	lysX
Ordered Locus Names:	TTHA1907

Organism

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Reference proteome] [HAMAP]

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus › Thermus thermophilus

Protein attributes

Sequence length	280 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.3
Catalytic activity	ATP + [lysW] + L-2-aminoadipate = ADP + phosphate + [lysW]-L-2-aminoadipate. Ref.3
Cofactor	Binds 2 magnesium ions per subunit By similarity.
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via AAA pathway; L-lysine from L-alpha-aminoadipate (Thermus route): step 1/5.
Subunit structure	Homodimer. Ref.1
Sequence similarities	Belongs to the RimK family. LysX subfamily. Contains 1 ATP-grasp domain.
Biophysicochemical properties	Kinetic parameters: KM=2.1 mM for alpha-aminoadipate Ref.3 KM=2.6 mM for ATP

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Lysine biosynthesis
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cellular protein modification process Inferred from electronic annotation. Source: InterPro lysine biosynthetic process via aminoadipic acid Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW acid-amino acid ligase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 280

280

Alpha-aminoadipate--LysW ligase LysX

PRO_0000391001

Regions

Domain

93 – 276

184

ATP-grasp

Nucleotide binding

169 – 178

10

ATP

Sites

Metal binding

237

1

Magnesium 1 By similarity

Metal binding

249

1

Magnesium 1 By similarity

Metal binding

249

1

Magnesium 2 By similarity

Metal binding

251

1

Magnesium 2 By similarity

Binding site

129

1

ATP

Binding site

194

1

ATP

Secondary structure

1

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280

Helix Strand Turn

Details...

Beta strand

2 – 8

7

Helix

11 – 23

13

Beta strand

27 – 31

5

Helix

32 – 34

3

Helix

44 – 46

3

Beta strand

51 – 54

4

Helix

59 – 71

13

Beta strand

76 – 78

3

Helix

80 – 87

8

Helix

89 – 98

10

Beta strand

106 – 111

6

Helix

112 – 122

11

Beta strand

124 – 129

6

Beta strand

140 – 142

3

Helix

145 – 153

9

Turn

161 – 164

4

Beta strand

166 – 170

5

Beta strand

179 – 184

6

Beta strand

187 – 193

7

Helix

216 – 228

13

Beta strand

232 – 241

10

Beta strand

244 – 251

8

Helix

259 – 263

5

Helix

267 – 277

11

Sequences

	Sequence		Length	Mass (Da)
	Q5SH23 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: B168629146AF1344	FASTA	280	30,718
	10 20 30 40 50 60 MLAILYDRIR PDERMLFERA EALGLPYKKV YVPALPMVLG ERPKELEGVT VALERCVSQS 70 80 90 100 110 120 RGLAAARYLT ALGIPVVNRP EVIEACGDKW ATSVALAKAG LPQPKTALAT DREEALRLME 130 140 150 160 170 180 AFGYPVVLKP VIGSWGRLLA KVTDRAAAEA LLEHKEVLGG FQHQLFYIQE YVEKPGRDIR 190 200 210 220 230 240 VFVVGERAIA AIYRRSAHWI TNTARGGQAE NCPLTEEVAR LSVKAAEAVG GGVVAVDLFE 250 260 270 280 SERGLLVNEV NHTMEFKNSV HTTGVDIPGE ILKYAWSLAS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB103032 Genomic DNA. Translation: BAC67243.1.
AP008226 Genomic DNA. Translation: BAD71730.1.

RefSeq

YP_145173.1. NC_006461.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	1-276	[»]

ProteinModelPortal

Q5SH23.

SMR

Q5SH23. Positions 1-280.

ModBase

Search...

Protein-protein interaction databases

STRING

300852.TTHA1907.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD71730; BAD71730; BAD71730.

GeneID

3167971.

KEGG

ttj:TTHA1907.

PATRIC

23958779. VBITheThe93045_1875.

Phylogenomic databases

eggNOG

COG0189.

HOGENOM

HOG000228553.

KO

K05827.

OMA

MEFKNSV.

ProtClustDB

CLSK2761981.

Enzyme and pathway databases

UniPathway

UPA00033; UER00035.

Family and domain databases

Gene3D

3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.

InterPro

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]

Pfam

PF08443. RimK. 1 hit.
[Graphical view]

SUPFAM

SSF52440. PreATP-grasp-like. 1 hit.

TIGRFAMs

TIGR02144. LysX_arch. 1 hit.
TIGR00768. rimK_fam. 1 hit.

PROSITE

PS50975. ATP_GRASP. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q5SH23.

Entry information

Entry name

LYSX_THET8

Accession

Primary (citable) accession number: Q5SH23
Secondary accession number(s): Q84BR0

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 19, 2010
Last sequence update:	December 21, 2004
Last modified:	May 1, 2013
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program