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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei17 – 171SubstrateUniRule annotation
Binding sitei50 – 501SubstrateUniRule annotation
Binding sitei70 – 701SubstrateUniRule annotation
Active sitei79 – 791Proton donor/acceptorUniRule annotation
Binding sitei167 – 1671SubstrateUniRule annotation
Sitei169 – 1691Important for catalytic activityUniRule annotation
Binding sitei200 – 2001SubstrateUniRule annotation
Sitei218 – 2181Important for catalytic activityUniRule annotation
Active sitei227 – 2271Proton donor/acceptorUniRule annotation

GO - Molecular functioni

  1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-480-MONOMER.
UniPathwayiUPA00034; UER00025.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
Short name:
DAP epimeraseUniRule annotation
Gene namesi
Name:dapFUniRule annotation
Ordered Locus Names:bll0477
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000002526 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 291291Diaminopimelate epimerasePRO_0000149822Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi79 ↔ 227

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi224911.bll0477.

Structurei

3D structure databases

ProteinModelPortaliQ89X45.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 152Substrate bindingUniRule annotation
Regioni79 – 813Substrate bindingUniRule annotation
Regioni218 – 2192Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
InParanoidiQ89X45.
KOiK01778.
OrthoDBiEOG6ND0M5.
PhylomeDBiQ89X45.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q89X45-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSALANHAFA KMNGIGNEIV VVDMRDSTAK VTPDDARAVA SAQGGVPYDQ
60 70 80 90 100
LMVLQKPRLD GTEAFISIYN NDGSEAGACG NGMRCVVRRI FEKTGQATAT
110 120 130 140 150
FETAAGLLNA WQGPAPDLYT VDMGVPKFGW QDIPLAEEFR DTRYIELQIG
160 170 180 190 200
PIDNPILHSP SVVSMGNPHA IFWVDDVNAY DLARFGPLLE NHPIFPERAN
210 220 230 240 250
ITLAHIVDRD HITIRTWERG AGLTRACGSA ACATAVAAAR LKRAERNVEI
260 270 280 290
TLPGGKLGIE WRERDDHVLM TGTATFEYEG NFDPALFAPA G
Length:291
Mass (Da):31,595
Last modified:June 20, 2003 - v1
Checksum:i58112A152FA5D6E3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC45742.1.
RefSeqiNP_767117.1. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC45742; BAC45742; BAC45742.
GeneIDi1053475.
KEGGibja:bll0477.
PATRICi21184419. VBIBraJap65052_0487.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC45742.1.
RefSeqiNP_767117.1. NC_004463.1.

3D structure databases

ProteinModelPortaliQ89X45.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224911.bll0477.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC45742; BAC45742; BAC45742.
GeneIDi1053475.
KEGGibja:bll0477.
PATRICi21184419. VBIBraJap65052_0487.

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
InParanoidiQ89X45.
KOiK01778.
OrthoDBiEOG6ND0M5.
PhylomeDBiQ89X45.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00025.
BioCyciBJAP224911:GJEJ-480-MONOMER.

Family and domain databases

HAMAPiMF_00197. DAP_epimerase.
InterProiIPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view]
PANTHERiPTHR31689. PTHR31689. 1 hit.
PfamiPF01678. DAP_epimerase. 2 hits.
[Graphical view]
TIGRFAMsiTIGR00652. DapF. 1 hit.
PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.

Entry informationi

Entry nameiDAPF_BRADU
AccessioniPrimary (citable) accession number: Q89X45
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2003
Last sequence update: June 20, 2003
Last modified: January 7, 2015
This is version 69 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

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.