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Entry version 144 (07 Apr 2021)
Sequence version 1 (01 Oct 1989)
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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg2+ or Mn2+ ion per subunit.By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: IMP biosynthesis via de novo pathway

This protein is involved in step 2 of the subpathway that synthesizes N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate.UniRule annotation
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Amidophosphoribosyltransferase (purF), Amidophosphoribosyltransferase (purF)
  2. Phosphoribosylamine--glycine ligase (purD), Phosphoribosylamine--glycine ligase (purD)
This subpathway is part of the pathway IMP biosynthesis via de novo pathway, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-alpha-D-ribose 1-diphosphate, the pathway IMP biosynthesis via de novo pathway and in Purine metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi283Magnesium or manganeseUniRule annotation1
Metal bindingi285Magnesium or manganeseUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi133 – 194ATPUniRule annotationAdd BLAST62

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLigase
Biological processPurine biosynthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
BSUB:BSU06530-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00074;UER00125

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Phosphoribosylamine--glycine ligaseUniRule annotation (EC:6.3.4.13UniRule annotation)
Alternative name(s):
GARSUniRule annotation
Glycinamide ribonucleotide synthetaseUniRule annotation
Phosphoribosylglycinamide synthetaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:purDUniRule annotation
Ordered Locus Names:BSU06530
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001514361 – 422Phosphoribosylamine--glycine ligaseAdd BLAST422

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P12039

PRoteomics IDEntifications database

More...
PRIDEi
P12039

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
224308.BSU06530

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1422
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P12039

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini107 – 313ATP-graspUniRule annotationAdd BLAST207

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the GARS family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0151, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P12039

Identification of Orthologs from Complete Genome Data

More...
OMAi
KATVCKY

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P12039

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.1490.20, 1 hit
3.90.600.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00138, GARS, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR011761, ATP-grasp
IPR013815, ATP_grasp_subdomain_1
IPR016185, PreATP-grasp_dom_sf
IPR020561, PRibGlycinamid_synth_ATP-grasp
IPR000115, PRibGlycinamide_synth
IPR020560, PRibGlycinamide_synth_C-dom
IPR037123, PRibGlycinamide_synth_C_sf
IPR020559, PRibGlycinamide_synth_CS
IPR020562, PRibGlycinamide_synth_N
IPR011054, Rudment_hybrid_motif

The PANTHER Classification System

More...
PANTHERi
PTHR43472, PTHR43472, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01071, GARS_A, 1 hit
PF02843, GARS_C, 1 hit
PF02844, GARS_N, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM01210, GARS_C, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51246, SSF51246, 1 hit
SSF52440, SSF52440, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00877, purD, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50975, ATP_GRASP, 1 hit
PS00184, GARS, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P12039-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNVLIIGKGG REHTLAWKAA QSSLVENVFA APGNDGMAAS AQLVNIEESD
60 70 80 90 100
HAGLVSFAKQ NQVGLTIVGP EVPLIEGLVD EFEKAGLHVF GPSKAAAIIE
110 120 130 140 150
GSKQFAKDLM KKYDIPTAEY ETFTSFDEAK AYVQEKGAPI VIKADGLAAG
160 170 180 190 200
KGVTVAMTEE EAIACLHDFL EDEKFGDASA SVVIEEYLSG EEFSLMAFVK
210 220 230 240 250
GEKVYPMVIA QDHKRAFDGD KGPNTGGMGA YSPVPQISEE TVRHAVETIV
260 270 280 290 300
KPAAKAMVQE GRSFTGVLYA GLMLTENGSK VIEFNARFGD PETQVVLPRM
310 320 330 340 350
ESDLVQVLLD LLDDKEVDLR WKDTAAVSVV LASEGYPESY AKGTPIGSLA
360 370 380 390 400
AETEQVVVFH AGTKAEGGEF VTNGGRVANV TAFDETFEAA RDRVYKAVDE
410 420
IFKPGLFFRK DIGARALKAA QK
Length:422
Mass (Da):45,280
Last modified:October 1, 1989 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i4EF390A85CC90FB2
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
J02732 Genomic DNA Translation: AAA22684.1
AF011544 Genomic DNA Translation: AAB72186.1
AL009126 Genomic DNA Translation: CAB12473.1

Protein sequence database of the Protein Information Resource

More...
PIRi
B29183, AJBSAG

NCBI Reference Sequences

More...
RefSeqi
NP_388535.1, NC_000964.3
WP_003242993.1, NZ_JNCM01000032.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
CAB12473; CAB12473; BSU_06530

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
938741

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
bsu:BSU06530

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|224308.179.peg.709

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02732 Genomic DNA Translation: AAA22684.1
AF011544 Genomic DNA Translation: AAB72186.1
AL009126 Genomic DNA Translation: CAB12473.1
PIRiB29183, AJBSAG
RefSeqiNP_388535.1, NC_000964.3
WP_003242993.1, NZ_JNCM01000032.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XCLX-ray2.10A1-422[»]
2XD4X-ray2.65A1-422[»]
SMRiP12039
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU06530

Proteomic databases

PaxDbiP12039
PRIDEiP12039

Genome annotation databases

EnsemblBacteriaiCAB12473; CAB12473; BSU_06530
GeneIDi938741
KEGGibsu:BSU06530
PATRICifig|224308.179.peg.709

Phylogenomic databases

eggNOGiCOG0151, Bacteria
InParanoidiP12039
OMAiKATVCKY
PhylomeDBiP12039

Enzyme and pathway databases

UniPathwayiUPA00074;UER00125
BioCyciBSUB:BSU06530-MONOMER

Family and domain databases

Gene3Di3.30.1490.20, 1 hit
3.90.600.10, 1 hit
HAMAPiMF_00138, GARS, 1 hit
InterProiView protein in InterPro
IPR011761, ATP-grasp
IPR013815, ATP_grasp_subdomain_1
IPR016185, PreATP-grasp_dom_sf
IPR020561, PRibGlycinamid_synth_ATP-grasp
IPR000115, PRibGlycinamide_synth
IPR020560, PRibGlycinamide_synth_C-dom
IPR037123, PRibGlycinamide_synth_C_sf
IPR020559, PRibGlycinamide_synth_CS
IPR020562, PRibGlycinamide_synth_N
IPR011054, Rudment_hybrid_motif
PANTHERiPTHR43472, PTHR43472, 1 hit
PfamiView protein in Pfam
PF01071, GARS_A, 1 hit
PF02843, GARS_C, 1 hit
PF02844, GARS_N, 1 hit
SMARTiView protein in SMART
SM01210, GARS_C, 1 hit
SUPFAMiSSF51246, SSF51246, 1 hit
SSF52440, SSF52440, 1 hit
TIGRFAMsiTIGR00877, purD, 1 hit
PROSITEiView protein in PROSITE
PS50975, ATP_GRASP, 1 hit
PS00184, GARS, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPUR2_BACSU
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P12039
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: April 7, 2021
This is version 144 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, 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
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