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Protein

Phosphoribosylamine--glycine ligase

Gene

purD

Organism
Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalytic activityi

ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N(1)-(5-phospho-D-ribosyl)glycinamide.UniRule annotation

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 Mg(2+) or Mn2+ ion per subunit.By similarity

Pathway: 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)
  2. 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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi282 – 2821Magnesium or manganeseUniRule annotation
Metal bindingi284 – 2841Magnesium or manganeseUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi133 – 19361ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Purine biosynthesis

Keywords - Ligandi

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

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.

Names & Taxonomyi

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
Gene namesi
Name:purDUniRule annotation
Ordered Locus Names:ZMO0299
OrganismiZymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
Taxonomic identifieri264203 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeZymomonas
ProteomesiUP000001173 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 417417Phosphoribosylamine--glycine ligasePRO_0000151507Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliQ9FDL5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 312206ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the GARS family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033463.
KOiK01945.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR016185. PreATP-grasp_dom.
IPR020561. PRibGlycinamid_synth_ATP-grasp.
IPR000115. PRibGlycinamide_synth.
IPR020560. PRibGlycinamide_synth_C-dom.
IPR020559. PRibGlycinamide_synth_CS.
IPR020562. PRibGlycinamide_synth_N.
IPR011054. Rudment_hybrid_motif.
[Graphical view]
PfamiPF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
[Graphical view]
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9FDL5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVLLIGTGG REHALAWKIA QSPSLDTFYA TTGNPGIAKL AKPADITVTD
60 70 80 90 100
HAAVVRFCQD NAIDLVVIGP EAPLVDGLGN SLRAASIAVF GPDKAAAQLE
110 120 130 140 150
GSKGFTKDLC ARYNIPTARY QRCRSAEEAK AALDNFSTPV VIKADGLAGG
160 170 180 190 200
KGVIIAESRL EAEQAIQDMT AGAFGKAGLE IVVEEFMQGE EASFFAISDG
210 220 230 240 250
ETVRPFGTAR DHKRVGDGDT GPNTGGMGAY SPATRLTADL EKRVMQEIVT
260 270 280 290 300
PTVQAMKEQG MPFVGILYAG LMLTSEGPKL IEYNARLGDP ECQVLMMRLE
310 320 330 340 350
SDILPLLYAA ATGKLQAQPE PTFSKDYAVT VVIAAQGYPA SPKKGGIITR
360 370 380 390 400
LNEAEANGAV VFQAGTTLDN QTLKANGGRV LNVTAKAADF NAARDLAYQA
410
VNVIDYPDGF WRGDIGL
Length:417
Mass (Da):44,044
Last modified:February 15, 2005 - v2
Checksum:iC31176955B0D9FC2
GO

Sequence cautioni

The sequence AAG02154.1 differs from that shown. Reason: Frameshift at positions 86, 99 and 123. Curated
The sequence AAV88923.2 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti235 – 2351R → S in AAG02154 (Ref. 1) Curated
Sequence conflicti395 – 3951D → Y in AAG02154 (Ref. 1) Curated
Sequence conflicti405 – 4051D → V in AAG02154 (Ref. 1) Curated
Sequence conflicti413 – 4131G → E in AAG02154 (Ref. 1) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF212041 Genomic DNA. Translation: AAG02154.1. Frameshift.
AE008692 Genomic DNA. Translation: AAV88923.2. Different initiation.
RefSeqiWP_011240234.1. NC_006526.2.
YP_162034.2. NC_006526.2.

Genome annotation databases

EnsemblBacteriaiAAV88923; AAV88923; ZMO0299.
KEGGizmo:ZMO0299.
PATRICi32565942. VBIZymMob102260_0286.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF212041 Genomic DNA. Translation: AAG02154.1. Frameshift.
AE008692 Genomic DNA. Translation: AAV88923.2. Different initiation.
RefSeqiWP_011240234.1. NC_006526.2.
YP_162034.2. NC_006526.2.

3D structure databases

ProteinModelPortaliQ9FDL5.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAV88923; AAV88923; ZMO0299.
KEGGizmo:ZMO0299.
PATRICi32565942. VBIZymMob102260_0286.

Phylogenomic databases

eggNOGiCOG0151.
HOGENOMiHOG000033463.
KOiK01945.

Enzyme and pathway databases

UniPathwayiUPA00074; UER00125.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
3.90.600.10. 1 hit.
HAMAPiMF_00138. GARS.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR016185. PreATP-grasp_dom.
IPR020561. PRibGlycinamid_synth_ATP-grasp.
IPR000115. PRibGlycinamide_synth.
IPR020560. PRibGlycinamide_synth_C-dom.
IPR020559. PRibGlycinamide_synth_CS.
IPR020562. PRibGlycinamide_synth_N.
IPR011054. Rudment_hybrid_motif.
[Graphical view]
PfamiPF01071. GARS_A. 1 hit.
PF02843. GARS_C. 1 hit.
PF02844. GARS_N. 1 hit.
[Graphical view]
SUPFAMiSSF51246. SSF51246. 1 hit.
SSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR00877. purD. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00184. GARS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Lee H.J., Kang H.S.
    Submitted (DEC-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 31821 / ZM4 / CP4.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 31821 / ZM4 / CP4.

Entry informationi

Entry nameiPUR2_ZYMMO
AccessioniPrimary (citable) accession number: Q9FDL5
Secondary accession number(s): Q5NQT1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2003
Last sequence update: February 15, 2005
Last modified: June 24, 2015
This is version 88 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.