Aspartate--tRNA ligase - Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

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Q52428 (SYD_PYRKO) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 106. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Aspartate--tRNA ligase
EC=6.1.1.12

Alternative name(s):
Aspartyl-tRNA synthetase
Short name=AspRS

Gene names

Name:	aspS
Ordered Locus Names:	TK0492

Organism

Pyrococcus kodakaraensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Thermococcus kodakaraensis (strain KOD1)) [Reference proteome] [HAMAP]

Taxonomic identifier

69014 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus ›

Protein attributes

Sequence length	438 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp). HAMAP-Rule MF_00044_A
Cofactor	Binds 3 magnesium ions per subunit. The first one is coordinated by ATP and H₂O.
Subunit structure	Homodimer.
Subcellular location	Cytoplasm HAMAP-Rule MF_00044_A.
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	aspartyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP aspartate-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP nucleic acid binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 438

438

Aspartate--tRNA ligase HAMAP-Rule MF_00044_A

PRO_0000111005

Sites

Metal binding

361

Magnesium 2

Metal binding

361

Magnesium 3

Metal binding

364

Magnesium 2

Experimental info

Sequence conflict

413

L → V in BAA08115. Ref.1

Secondary structure

438

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q52428 [UniParc].

Last modified March 29, 2005. Version 2.
Checksum: E03C8766ADD2209A
Show »

FASTA

438

50,910

        10         20         30         40         50         60 
MYRTHYSSEI TEELNGQKVK VAGWVWEVKD LGGIKFLWIR DRDGIVQITA PKKKVDPELF 

        70         80         90        100        110        120 
KLIPKLRSED VVAVEGVVNF TPKAKLGFEI LPEKIVVLNR AETPLPLDPT GKVKAELDTR 

       130        140        150        160        170        180 
LDNRFMDLRR PEVMAIFKIR SSVFKAVRDF FHENGFIEIH TPKIIATATE GGTELFPMKY 

       190        200        210        220        230        240 
FEEDAFLAQS PQLYKQIMMA SGLDRVYEIA PIFRAEEHNT TRHLNEAWSI DSEMAFIEDE 

       250        260        270        280        290        300 
EEVMSFLERL VAHAINYVRE HNAKELDILN FELEEPKLPF PRVSYDKALE ILGDLGKEIP 

       310        320        330        340        350        360 
WGEDIDTEGE RLLGKYMMEN ENAPLYFLYQ YPSEAKPFYI MKYDNKPEIC RAFDLEYRGV 

       370        380        390        400        410        420 
EISSGGQREH RHDILVEQIK EKGLNPESFE FYLKAFRYGM PPHGGFGLGA ERLIKQMLDL 

       430 
PNIREVILFP RDRRRLTP

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Aspartyl-tRNA synthetase of the hyperthermophilic archaeon Pyrococcus sp. KOD1 has a chimerical structure of eukaryotic and bacterial enzymes." Imanaka T., Lee S., Takagi M., Fujiwara S. Gene 164:153-156(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[2]	"Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes." Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T. Genome Res. 15:352-363(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-918 / JCM 12380 / KOD1.
[3]	"Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation." Schmitt E., Moulinier L., Fujiwara S., Imanaka T., Thierry J.-C., Moras D. EMBO J. 17:5227-5237(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). Strain: ATCC BAA-918 / JCM 12380 / KOD1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D45167 Genomic DNA. Translation: BAA08115.1.
AP006878 Genomic DNA. Translation: BAD84681.1.

RefSeq

YP_182905.1. NC_006624.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B8A	X-ray	1.90	A/B	1-438	[»]
3NEL	X-ray	1.95	A/B	1-438	[»]
3NEM	X-ray	1.89	A/B	1-438	[»]
3NEN	X-ray	2.40	A/B	1-438	[»]

ProteinModelPortal

Q52428.

SMR

Q52428. Positions 1-438.

ModBase

Search...

Protein-protein interaction databases

STRING

69014.TK0492.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAD84681; BAD84681; TK0492.

GeneID

3235903.

KEGG

tko:TK0492.

Phylogenomic databases

eggNOG

COG0017.

HOGENOM

HOG000226032.

K01876.

OMA

RVKVAGW.

ProtClustDB

PRK05159.

Enzyme and pathway databases

BRENDA

6.1.1.12. 5246.

SABIO-RK

Q52428.

Family and domain databases

Gene3D

2.40.50.140. 1 hit.

HAMAP

MF_00044_A. Asp_tRNA_synth_A.

InterPro

IPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR020780. Asp-tRNA-synth_arc.
IPR004523. Asp-tRNA_synthase.
IPR002312. Asp/Asn-tRNA-synth_IIb.
IPR012340. NA-bd_OB-fold.
IPR004365. NA-bd_OB_tRNA-helicase.
[Graphical view]

PANTHER

PTHR22594. PTHR22594. 1 hit.
PTHR22594:SF10. PTHR22594:SF10. 1 hit.

Pfam

PF00152. tRNA-synt_2. 1 hit.
PF01336. tRNA_anti. 1 hit.
[Graphical view]

PRINTS

PR01042. TRNASYNTHASP.

SUPFAM

SSF50249. Nucleic_acid_OB. 1 hit.

TIGRFAMs

TIGR00458. aspS_nondisc. 1 hit.

PROSITE

PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q52428.

Entry information

Entry name

SYD_PYRKO

Accession

Primary (citable) accession number: Q52428
Secondary accession number(s): Q5JD76

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	March 29, 2005
Last modified:	May 1, 2013
This is version 106 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents