D-alanine--D-alanine ligase precursor - Calditerrivibrio nitroreducens (strain DSM 19672 / NBRC 101217 / Yu37-1)

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E4TFX3 (E4TFX3_CALNY) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 22. History...

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

Third-party data

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

Names and origin

Protein names

Recommended name:
D-alanine--D-alanine ligase HAMAP-Rule MF_00047
EC=6.3.2.4 HAMAP-Rule MF_00047

Alternative name(s):
D-Ala-D-Ala ligase HAMAP-Rule MF_00047
D-alanylalanine synthetase HAMAP-Rule MF_00047

Gene names

Name:	ddl HAMAP-Rule MF_00047
Ordered Locus Names:	Calni_1723 EMBL ADR19629.1

Organism

Calditerrivibrio nitroreducens (strain DSM 19672 / NBRC 101217 / Yu37-1) [Complete proteome] [HAMAP] EMBL ADR19629.1

Taxonomic identifier

768670 [NCBI]

Taxonomic lineage

Bacteria › Deferribacteres › Deferribacterales › Deferribacteraceae ›

Protein attributes

Sequence length	298 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Cell wall formation By similarity. HAMAP-Rule MF_00047 SAAS SAAS005905
Catalytic activity	ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP-Rule MF_00047 SAAS SAAS005905
Cofactor	Binds 2 magnesium or manganese ions per subunit By similarity. HAMAP-Rule MF_00047 SAAS SAAS005905
Pathway	Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_00047 SAAS SAAS005905
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_00047 SAAS SAAS005905.
Sequence similarities	Belongs to the D-alanine--D-alanine ligase family. HAMAP-Rule MF_00047 Contains 1 ATP-grasp domain. HAMAP-Rule MF_00047 SAAS SAAS005905

Ontologies

Keywords
Biological process	Cell shape Cell wall biogenesis/degradation HAMAP-Rule MF_00047 SAAS SAAS005905 Peptidoglycan synthesis HAMAP-Rule MF_00047 SAAS SAAS005905
Cellular component	Cytoplasm HAMAP-Rule MF_00047 SAAS SAAS005905
Ligand	ATP-binding HAMAP-Rule MF_00047 SAAS SAAS005905 Magnesium HAMAP-Rule MF_00047 SAAS SAAS005905 Manganese HAMAP-Rule MF_00047 SAAS SAAS005905 Metal-binding HAMAP-Rule MF_00047 SAAS SAAS005905 Nucleotide-binding
Molecular function	Ligase HAMAP-Rule MF_00047 SAAS SAAS005905 EMBL ADR19629.1
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	peptidoglycan biosynthetic process Inferred from electronic annotation. Source: HAMAP regulation of cell shape Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cell wall Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP D-alanine-D-alanine ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP manganese ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Regions

Domain

103 – 291

189

ATP-grasp By similarity HAMAP-Rule MF_00047

Nucleotide binding

129 – 178

ATP By similarity HAMAP-Rule MF_00047

Sites

Metal binding

246

Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047

Metal binding

258

Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047

Metal binding

258

Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047

Metal binding

260

Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047

Sequences

Sequence

Length

Mass (Da)

Tools

E4TFX3 [UniParc].

Last modified February 8, 2011. Version 1.
Checksum: 96A35AD932B14A8A
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FASTA

298

33,622

        10         20         30         40         50         60 
MHSDKIAVLY GGLSSERDVS IKTGNGIYNA LLRKGFKNSF LLDVDWSLPE KLIKHKPDFC 

        70         80         90        100        110        120 
YIALHGRYGE DGTVQGLLEY MRIPYNGPGV TASAISFDKV ITKKILKSVN IPTADYFEYK 

       130        140        150        160        170        180 
NEQSSPFYPC VVKPAREGST IGVTIVYEDK EFIPAIEDAK KYDNKIIVER FIKGKELTIS 

       190        200        210        220        230        240 
IIDDLVLPII WIKPKKGFYD YTSKYTKGMT EYLFETGLNA KEEEMVKKVA KDAYEVVGCE 

       250        260        270        280        290 
GASRVDIIYD GDIPNVLEIN TLPGMTETSL LPNAAAKYGI AYDELVEMLY FKGKNRYE

« Hide

References

[1]

"The complete genome of chromosome of Calditerrivibrio nitroreducens DSM 19672."
US DOE Joint Genome Institute (JGI-PGF)
Lucas S., Copeland A., Lapidus A., Bruce D., Goodwin L., Pitluck S., Kyrpides N., Mavromatis K., Ivanova N., Mikhailova N., Zeytun A., Brettin T., Detter J.C., Tapia R., Han C., Land M., Hauser L., Markowitz V.

Eisen J.A.
Submitted (NOV-2010) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 19672.

[2]

"Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1)."
Pitluck S., Sikorski J., Zeytun A., Lapidus A., Nolan M., Lucas S., Hammon N., Deshpande S., Cheng J.F., Tapia R., Han C., Goodwin L., Liolios K., Pagani I., Ivanova N., Mavromatis K., Pati A., Chen A.

Land M.
Stand. Genomic Sci. 4:54-62(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 19672 / NBRC 101217 / Yu37-1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP002347 Genomic DNA. Translation: ADR19629.1.
RefSeq	YP_004051792.1. NC_014758.1.
3D structure databases
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ADR19629; ADR19629; Calni_1723.
GeneID	10009760.
KEGG	cni:Calni_1723.
PATRIC	45191248. VBICalNit163602_1813.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	HOG000011592.
KO	K01921.
OMA	WREAARY.
Enzyme and pathway databases
BioCyc	CNIT768670:GHD1-1762-MONOMER.
UniPathway	UPA00219.
Family and domain databases
Gene3D	3.30.1490.20. 1 hit. 3.30.470.20. 2 hits. 3.40.50.20. 1 hit.
HAMAP	MF_00047. Dala_Dala_lig.
InterPro	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]
PANTHER	PTHR23132. PTHR23132. 1 hit.
Pfam	PF07478. Dala_Dala_lig_C. 1 hit. PF01820. Dala_Dala_lig_N. 2 hits. [Graphical view]
SUPFAM	SSF52440. PreATP-grasp-like. 1 hit.
TIGRFAMs	TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITE	PS50975. ATP_GRASP. 1 hit. PS00843. DALA_DALA_LIGASE_1. 1 hit. PS00844. DALA_DALA_LIGASE_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

E4TFX3_CALNY

Accession

Primary (citable) accession number: E4TFX3

Entry history

Integrated into UniProtKB/TrEMBL:	February 8, 2011
Last sequence update:	February 8, 2011
Last modified:	May 1, 2013
This is version 22 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

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

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information