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B4RCE2

- DAPF_PHEZH

UniProt

B4RCE2 - DAPF_PHEZH

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Phenylobacterium zucineum (strain HLK1)
Status
Reviewed - 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 sitei68 – 681SubstrateUniRule annotation
Active sitei77 – 771Proton donor/acceptorUniRule annotation
Binding sitei162 – 1621SubstrateUniRule annotation
Sitei164 – 1641Important for catalytic activityUniRule annotation
Binding sitei195 – 1951SubstrateUniRule annotation
Sitei213 – 2131Important for catalytic activityUniRule annotation
Active sitei222 – 2221Proton 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

BioCyciPZUC450851:GHUG-129-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:PHZ_c0127
OrganismiPhenylobacterium zucineum (strain HLK1)
Taxonomic identifieri450851 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaePhenylobacterium
ProteomesiUP000001868: 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 – 277277Diaminopimelate epimerasePRO_1000099255Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi77 ↔ 222

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi450851.PHZ_c0127.

Structurei

3D structure databases

ProteinModelPortaliB4RCE2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 152Substrate bindingUniRule annotation
Regioni77 – 793Substrate bindingUniRule annotation
Regioni213 – 2142Substrate bindingUniRule annotation
Regioni223 – 2242Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiKMRIFNN.
OrthoDBiEOG6ND0M5.

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.

B4RCE2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSAAMGRPFL KMNGLGNDFV VVETRSAPFE PTAAQVRAIA DRATGIGCDQ
60 70 80 90 100
LIAVDPAEGA DAHVRFWNAD GEEVGACGNG TRCVGWLLMQ SSGKDEAVIE
110 120 130 140 150
TRAGRLVATR AGERLVSVDM GPPRLEWNEI PLAEPHDTRA LDVVLYHHAD
160 170 180 190 200
LMAPPGCVSM GNPHVVFFVP DAEQAPAAEA GPAIEGHPLF PEHVNVGFAQ
210 220 230 240 250
VKAPDRIRLR VWERGAGLTK ACGTGACAAM VAASRRGLIG RHATMELDGG
260 270
ELFVEWRADG HVIMTGPAAV DFQGELP
Length:277
Mass (Da):29,372
Last modified:September 23, 2008 - v1
Checksum:i1EF73A28BBD0AE80
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000747 Genomic DNA. Translation: ACG76541.1.
RefSeqiWP_012520689.1. NC_011144.1.
YP_002128970.1. NC_011144.1.

Genome annotation databases

EnsemblBacteriaiACG76541; ACG76541; PHZ_c0127.
GeneIDi6789615.
KEGGipzu:PHZ_c0127.
PATRICi22922770. VBIPheZuc44517_0482.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000747 Genomic DNA. Translation: ACG76541.1 .
RefSeqi WP_012520689.1. NC_011144.1.
YP_002128970.1. NC_011144.1.

3D structure databases

ProteinModelPortali B4RCE2.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 450851.PHZ_c0127.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACG76541 ; ACG76541 ; PHZ_c0127 .
GeneIDi 6789615.
KEGGi pzu:PHZ_c0127.
PATRICi 22922770. VBIPheZuc44517_0482.

Phylogenomic databases

eggNOGi COG0253.
HOGENOMi HOG000220466.
KOi K01778.
OMAi KMRIFNN.
OrthoDBi EOG6ND0M5.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci PZUC450851:GHUG-129-MONOMER.

Family and domain databases

HAMAPi MF_00197. DAP_epimerase.
InterProi IPR018510. DAP_epimerase_AS.
IPR001653. DAP_epimerase_DapF.
[Graphical view ]
PANTHERi PTHR31689. PTHR31689. 1 hit.
Pfami PF01678. DAP_epimerase. 2 hits.
[Graphical view ]
TIGRFAMsi TIGR00652. DapF. 1 hit.
PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete genome of Phenylobacterium zucineum - a novel facultative intracellular bacterium isolated from human erythroleukemia cell line K562."
    Luo Y., Xu X., Ding Z., Liu Z., Zhang B., Yan Z., Sun J., Hu S., Hu X.
    BMC Genomics 9:386-386(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HLK1.

Entry informationi

Entry nameiDAPF_PHEZH
AccessioniPrimary (citable) accession number: B4RCE2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: September 23, 2008
Last modified: October 29, 2014
This is version 43 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