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B1ZDT1

- DAPF_METPB

UniProt

B1ZDT1 - DAPF_METPB

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Methylobacterium populi (strain ATCC BAA-705 / NCIMB 13946 / BJ001)
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 sitei49 – 491SubstrateUniRule annotation
Binding sitei69 – 691SubstrateUniRule annotation
Active sitei78 – 781Proton donor/acceptorUniRule annotation
Binding sitei171 – 1711SubstrateUniRule annotation
Sitei173 – 1731Important for catalytic activityUniRule annotation
Binding sitei205 – 2051SubstrateUniRule annotation
Sitei223 – 2231Important for catalytic activityUniRule annotation
Active sitei232 – 2321Proton 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

BioCyciMPOP441620:GHMI-2894-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:Mpop_2842
OrganismiMethylobacterium populi (strain ATCC BAA-705 / NCIMB 13946 / BJ001)
Taxonomic identifieri441620 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesMethylobacteriaceaeMethylobacterium
ProteomesiUP000007136: 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 – 296296Diaminopimelate epimerasePRO_1000099246Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi78 ↔ 232

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi441620.Mpop_2842.

Structurei

3D structure databases

ProteinModelPortaliB1ZDT1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni78 – 803Substrate bindingUniRule annotation
Regioni223 – 2242Substrate bindingUniRule annotation
Regioni233 – 2342Substrate 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.

B1ZDT1-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSPLANRRFL KMHGAGNAIV VLDLRGTSIR VAPAEARAIA ADAHSRFDQL
60 70 80 90 100
MVVHDPVTPG TDAFMRIYNT DGSESGACGN GTRCVGYALL DDPAMARPAE
110 120 130 140 150
NGCLTLETKA GLVAVKRVTD RSFTVDMGQP RLRWDEIPLA EPFPDTRRIE
160 170 180 190 200
LQVGPIDDPI LHSPAAVSMG NPHAIFFVER DPDTFDLGRI GPLLEAHPIF
210 220 230 240 250
PERANISIAQ VTSRDTIKLR VWERGAGLTL ACGTAACATV VAAARLRMIG
260 270 280 290
RAARVALPGG ELSIEWRADD HVLMTGPVFL EGEGSLSPDL FAGLDG
Length:296
Mass (Da):31,724
Last modified:May 20, 2008 - v1
Checksum:i5CDA06C1C7121F59
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001029 Genomic DNA. Translation: ACB80997.1.
RefSeqiWP_012454719.1. NC_010725.1.
YP_001925532.1. NC_010725.1.

Genome annotation databases

EnsemblBacteriaiACB80997; ACB80997; Mpop_2842.
GeneIDi6310250.
KEGGimpo:Mpop_2842.
PATRICi22562958. VBIMetPop124700_2888.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001029 Genomic DNA. Translation: ACB80997.1 .
RefSeqi WP_012454719.1. NC_010725.1.
YP_001925532.1. NC_010725.1.

3D structure databases

ProteinModelPortali B1ZDT1.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 441620.Mpop_2842.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACB80997 ; ACB80997 ; Mpop_2842 .
GeneIDi 6310250.
KEGGi mpo:Mpop_2842.
PATRICi 22562958. VBIMetPop124700_2888.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci MPOP441620:GHMI-2894-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 sequence of chromosome of Methylobacterium populi BJ001."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.
    , Kyrpides N., Mikhailova N., Marx C., Richardson P.
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-705 / NCIMB 13946 / BJ001.

Entry informationi

Entry nameiDAPF_METPB
AccessioniPrimary (citable) accession number: B1ZDT1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: October 29, 2014
This is version 47 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

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3