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A5VAG4

- DAPF_SPHWW

UniProt

A5VAG4 - DAPF_SPHWW

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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
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 sitei13 – 131SubstrateUniRule annotation
Binding sitei47 – 471SubstrateUniRule annotation
Binding sitei65 – 651SubstrateUniRule annotation
Active sitei74 – 741Proton donor/acceptorUniRule annotation
Binding sitei149 – 1491SubstrateUniRule annotation
Sitei151 – 1511Important for catalytic activityUniRule annotation
Binding sitei182 – 1821SubstrateUniRule annotation
Sitei200 – 2001Important for catalytic activityUniRule annotation
Active sitei209 – 2091Proton 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

BioCyciSWIT392499:GHZK-2962-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:Swit_2928
OrganismiSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
Taxonomic identifieri392499 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas
ProteomesiUP000001989: 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 – 274274Diaminopimelate epimerasePRO_1000011973Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi74 ↔ 209

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiA5VAG4.

Interactioni

Protein-protein interaction databases

STRINGi392499.Swit_2928.

Structurei

3D structure databases

ProteinModelPortaliA5VAG4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni10 – 112Substrate bindingUniRule annotation
Regioni74 – 763Substrate bindingUniRule annotation
Regioni200 – 2012Substrate bindingUniRule annotation
Regioni210 – 2112Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the diaminopimelate epimerase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0253.
HOGENOMiHOG000220466.
KOiK01778.
OMAiLIVEPPY.
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.

A5VAG4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQVRFHKMHG LGNDFVVIDA RATAPVEMTA ARARALADRK TGVGCDQLIL
60 70 80 90 100
LEPSAVADAR MRIFNADGSE VEACGNATRC VVSLLGGSAR IETVAGLLEG
110 120 130 140 150
RSADGQVSVE LGEPRFDWDA IPLAYAMDTR AMPVAWEELE APMAANVGNP
160 170 180 190 200
HVVFFVPETD AVALDRLGPR IETDPLFPAR INVNVATVDD RANIRLRVWE
210 220 230 240 250
RGVGLTDACG TGACATAVSA IRAGLVDSPV RVTLPGGPLT IDWAPGRPIV
260 270
MTGPATHVFT AETDLSAFGA DSRG
Length:274
Mass (Da):28,927
Last modified:July 10, 2007 - v1
Checksum:iBCCDAFE707FFEC04
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000699 Genomic DNA. Translation: ABQ69280.1.
RefSeqiYP_001263418.1. NC_009511.1.

Genome annotation databases

EnsemblBacteriaiABQ69280; ABQ69280; Swit_2928.
GeneIDi5199935.
KEGGiswi:Swit_2928.
PATRICi23685041. VBISphWit55028_3464.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000699 Genomic DNA. Translation: ABQ69280.1 .
RefSeqi YP_001263418.1. NC_009511.1.

3D structure databases

ProteinModelPortali A5VAG4.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 392499.Swit_2928.

Proteomic databases

PRIDEi A5VAG4.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABQ69280 ; ABQ69280 ; Swit_2928 .
GeneIDi 5199935.
KEGGi swi:Swit_2928.
PATRICi 23685041. VBISphWit55028_3464.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00025 .
BioCyci SWIT392499:GHZK-2962-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RW1 / DSM 6014 / JCM 10273.

Entry informationi

Entry nameiDAPF_SPHWW
AccessioniPrimary (citable) accession number: A5VAG4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 10, 2007
Last modified: October 29, 2014
This is version 51 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