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Q5YRY7

- DDL_NOCFA

UniProt

Q5YRY7 - DDL_NOCFA

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Nocardia farcinica (strain IFM 10152)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotation

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotation

Cofactori

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi308 – 3081Magnesium or manganese 1UniRule annotation
Metal bindingi320 – 3201Magnesium or manganese 1UniRule annotation
Metal bindingi320 – 3201Magnesium or manganese 2UniRule annotation
Metal bindingi322 – 3221Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi176 – 23156ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciNFAR247156:GJ9T-4263-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:NFA_42050
OrganismiNocardia farcinica (strain IFM 10152)
Taxonomic identifieri247156 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeNocardia
ProteomesiUP000006820: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 363363D-alanine--D-alanine ligasePRO_0000341140Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi247156.nfa42050.

Structurei

3D structure databases

ProteinModelPortaliQ5YRY7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini148 – 353206ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG1181.
KOiK01921.
OMAiIECGVLG.
OrthoDBiEOG64BQ73.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR000291. D-Ala_lig_Van_CS.
IPR005905. D_ala_D_ala.
IPR011095. Dala_Dala_lig_C.
IPR011127. Dala_Dala_lig_N.
IPR016185. PreATP-grasp_dom.
[Graphical view]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5YRY7-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTNRIRVAVV FGGRSNEHAV SCVSAGSVLR HLDPTRYEAV PIGITPQGGW
60 70 80 90 100
VLANSDVAAI GLSHEALPSV DAGGTALTLT ADPTRGGELV ALDDAGAVLG
110 120 130 140 150
TVDVVFPILH GPFGEDGTLQ GMLELAGVPY VGPGVLASAA GMDKEFTKKL
160 170 180 190 200
LAAEGLPVGT QVVLRPGTAT LTEEQRERLG LPVFVKPARA GSSIGITKVD
210 220 230 240 250
DWAALDTAIA AAREHDPKVI VEAGIVGREV ECGVLEFPDG RISASVLAEI
260 270 280 290 300
RMPEGDGPQF YDFDTKYLDD VCEFDVPAKL DDDIAEQVRE LAVRAFQALD
310 320 330 340 350
CQGLARVDFF VTADGPVINE INTMPGFTSI SMYPRMWEAT GIDYGTLVST
360
LIETALARGT GLR
Length:363
Mass (Da):38,228
Last modified:November 23, 2004 - v1
Checksum:iEB08DE40900C2449
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP006618 Genomic DNA. Translation: BAD59054.1.
RefSeqiYP_120418.1. NC_006361.1.

Genome annotation databases

EnsemblBacteriaiBAD59054; BAD59054; NFA_42050.
GeneIDi3109811.
KEGGinfa:nfa42050.
PATRICi22737950. VBINocFar94200_4204.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP006618 Genomic DNA. Translation: BAD59054.1 .
RefSeqi YP_120418.1. NC_006361.1.

3D structure databases

ProteinModelPortali Q5YRY7.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 247156.nfa42050.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD59054 ; BAD59054 ; NFA_42050 .
GeneIDi 3109811.
KEGGi nfa:nfa42050.
PATRICi 22737950. VBINocFar94200_4204.

Phylogenomic databases

eggNOGi COG1181.
KOi K01921.
OMAi IECGVLG.
OrthoDBi EOG64BQ73.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci NFAR247156:GJ9T-4263-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR000291. D-Ala_lig_Van_CS.
IPR005905. D_ala_D_ala.
IPR011095. Dala_Dala_lig_C.
IPR011127. Dala_Dala_lig_N.
IPR016185. PreATP-grasp_dom.
[Graphical view ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: IFM 10152.

Entry informationi

Entry nameiDDL_NOCFA
AccessioniPrimary (citable) accession number: Q5YRY7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: November 23, 2004
Last modified: October 29, 2014
This is version 75 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

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