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Q8ZIE7

- DDL_YERPE

UniProt

Q8ZIE7 - DDL_YERPE

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Yersinia pestis
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

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 bindingi257 – 2571Magnesium or manganese 1UniRule annotation
Metal bindingi270 – 2701Magnesium or manganese 1UniRule annotation
Metal bindingi270 – 2701Magnesium or manganese 2UniRule annotation
Metal bindingi272 – 2721Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18956ATPUniRule 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

BioCyciYPES214092:GKDD-551-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
Synonyms:ddlB
Ordered Locus Names:YPO0557, y3624, YP_3627
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000000815: Chromosome, UP000001019: Chromosome, UP000002490: 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 – 306306D-alanine--D-alanine ligasePRO_0000177912Add
BLAST

Proteomic databases

PRIDEiQ8ZIE7.

Interactioni

Protein-protein interaction databases

IntActiQ8ZIE7. 3 interactions.
STRINGi214092.YPO0557.

Structurei

Secondary structure

1
306
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 95
Helixi16 – 3318
Beta strandi37 – 415
Turni42 – 443
Helixi47 – 493
Turni50 – 545
Beta strandi57 – 604
Turni65 – 673
Beta strandi68 – 703
Helixi71 – 799
Beta strandi83 – 853
Helixi88 – 947
Helixi97 – 10610
Beta strandi114 – 1185
Helixi119 – 1224
Helixi127 – 1348
Helixi135 – 1373
Beta strandi139 – 1479
Beta strandi155 – 1573
Helixi160 – 1623
Helixi163 – 1719
Beta strandi175 – 1817
Beta strandi187 – 1937
Beta strandi201 – 2044
Beta strandi222 – 2265
Helixi231 – 24616
Turni247 – 2493
Beta strandi252 – 2609
Beta strandi266 – 2749
Beta strandi278 – 2814
Helixi282 – 2909
Helixi294 – 30310

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3V4ZX-ray2.69A/B1-306[»]
ProteinModelPortaliQ8ZIE7.
SMRiQ8ZIE7. Positions 1-306.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini101 – 303203ATP-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.
HOGENOMiHOG000011592.
KOiK01921.
OMAiEDPARES.
OrthoDBiEOG6ND0KB.

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.

Q8ZIE7-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAEKVAVLLG GTSAEREVSL LSGQAVLAGL KEAGIDAYGV DTKDFPVTQL
60 70 80 90 100
KEQGFDKVFI ALHGRGGEDG TLQGVLEFLQ LPYTGSGVMA SALTMDKLRT
110 120 130 140 150
KLVWQALGLP ISPYVALNRQ QFETLSPEEL VACVAKLGLP LIVKPSHEGS
160 170 180 190 200
SVGMSKVDHA SELQKALVEA FQHDSDVLIE KWLSGPEFTV AILGDEVLPS
210 220 230 240 250
IRIQPPGVFY DYDAKYLSDK TQYFCPSGLS DESEQQLAAL ALQAYHALDC
260 270 280 290 300
SGWGRVDVMQ DRDGHFYLLE VNTSPGMTSH SLVPMAARQY GLSFSQLVAR

ILMLAD
Length:306
Mass (Da):33,150
Last modified:March 1, 2002 - v1
Checksum:iC78CFF3D2E11F846
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL590842 Genomic DNA. Translation: CAL19236.1.
AE009952 Genomic DNA. Translation: AAM87172.1.
AE017042 Genomic DNA. Translation: AAS63775.1.
PIRiAB0069.
RefSeqiNP_670921.1. NC_004088.1.
NP_994898.1. NC_005810.1.
YP_002345628.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM87172; AAM87172; y3624.
AAS63775; AAS63775; YP_3627.
GeneIDi1148571.
1173401.
2763379.
KEGGiype:YPO0557.
ypk:y3624.
ypm:YP_3627.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL590842 Genomic DNA. Translation: CAL19236.1 .
AE009952 Genomic DNA. Translation: AAM87172.1 .
AE017042 Genomic DNA. Translation: AAS63775.1 .
PIRi AB0069.
RefSeqi NP_670921.1. NC_004088.1.
NP_994898.1. NC_005810.1.
YP_002345628.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3V4Z X-ray 2.69 A/B 1-306 [» ]
ProteinModelPortali Q8ZIE7.
SMRi Q8ZIE7. Positions 1-306.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi Q8ZIE7. 3 interactions.
STRINGi 214092.YPO0557.

Proteomic databases

PRIDEi Q8ZIE7.

Protocols and materials databases

DNASUi 1148571.
Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAM87172 ; AAM87172 ; y3624 .
AAS63775 ; AAS63775 ; YP_3627 .
GeneIDi 1148571.
1173401.
2763379.
KEGGi ype:YPO0557.
ypk:y3624.
ypm:YP_3627.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011592.
KOi K01921.
OMAi EDPARES.
OrthoDBi EOG6ND0KB.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci YPES214092:GKDD-551-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: CO-92 / Biovar Orientalis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: KIM10+ / Biovar Mediaevalis.
  3. "Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
    Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R.
    , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
    DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 91001 / Biovar Mediaevalis.

Entry informationi

Entry nameiDDL_YERPE
AccessioniPrimary (citable) accession number: Q8ZIE7
Secondary accession number(s): Q0WJB0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: March 1, 2002
Last modified: October 29, 2014
This is version 102 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

3D-structure, Complete proteome, 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

External Data

Dasty 3