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B2RMB9 (DAPA_PORG3) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 27. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Dihydrodipicolinate synthase
Short name=DHDPS
EC=4.2.1.52
Gene names
Name:dapA
Ordered Locus Names:PGN_1996
OrganismPorphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257) [Complete proteome] [HAMAP]
Taxonomic identifier431947 [NCBI]
Taxonomic lineageBacteria › Bacteroidetes › Bacteroidia › Bacteroidales › Porphyromonadaceae › Porphyromonas

Protein attributes

Sequence length297 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Catalytic activity

L-aspartate 4-semialdehyde + pyruvate = dihydrodipicolinate + 2 H2O. HAMAP MF_00418

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. HAMAP MF_00418

Subunit structure

Homotetramer By similarity. HAMAP MF_00418

Subcellular location

Cytoplasm By similarity HAMAP MF_00418.

Sequence similarities

Belongs to the DHDPS family.

Ontologies

Keywords
   Biological processAmino-acid biosynthesis
Diaminopimelate biosynthesis
Lysine biosynthesis
   Cellular componentCytoplasm
   LigandSchiff base
   Molecular functionLyase
   Technical termComplete proteome
Gene Ontology (GO)
   Biological processdiaminopimelate biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular functiondihydrodipicolinate synthase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 297297Dihydrodipicolinate synthase HAMAP MF_00418
PRO_1000124057

Regions

Region52 – 532Pyruvate binding By similarity

Sites

Active site1661Schiff-base intermediate with substrate By similarity
Binding site1101Pyruvate By similarity
Site1371Involved in proton transfer during cleavage By similarity

Sequences

Sequence LengthMass (Da)Tools
B2RMB9 [UniParc].

Last modified July 1, 2008. Version 1.
Checksum: BEE909A69F9EA420

FASTA29732,617
        10         20         30         40         50         60 
MDRAQLRGMG VALITPFDEK GEVDHESLRL LADYQVAGGA DYIVALGTTG ESPTIEEAER 

        70         80         90        100        110        120 
SAILQTVREA VAGRCPIIVG AGGNYTERLV NRIQAMDKTG VDAILSVAPY YNKPTQEGIY 

       130        140        150        160        170        180 
RHYRTLAEST DTSIILYNVP GRTGVNIKSE TTLRLATDCP NIIGIKEASG NVDQVRAIVL 

       190        200        210        220        230        240 
EKPDPFIVLS GDDHLSLSFI KEGAEGVISV IGNAYPELFS RLIHLCLENR FEEAETIQQR 

       250        260        270        280        290 
LEGMCYLMFV DGNPAGIKEL LYQKGLIRHN ILRLPLVSAS DSTSTLIARV RNQIEQR

« Hide

References

[1]"Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis."
Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., Nakayama K.
DNA Res. 15:215-225(2008) [PubMed: 18524787] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 33277 / DSM 20709 / JCM 12257.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AP009380 Genomic DNA. Translation: BAG34514.1.
RefSeqYP_001930111.1. NC_010729.1.

3D structure databases

ProteinModelPortalB2RMB9.
ModBaseSearch...

Protein-protein interaction databases

STRINGB2RMB9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID6328924.
GenomeReviewsGene locus PGN_1996 in contig AP009380_GR.
KEGGpgn:PGN_1996.
PATRIC22976947. VBIPorGin26334_1962.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHBG358848.
OMACEMEDSN.
ProtClustDBCLSK2306166.

Family and domain databases

HAMAPMF_00418. DapA.
[Tree]
InterProIPR013785. Aldolase_TIM.
IPR002220. Dihydrodipicolinate_synth-like.
IPR020625. Dihydrodipicolinate_synth_AS.
IPR005263. Dihydrodipicolinate_synth_DapA.
[Graphical view]
Gene3DG3DSA:3.20.20.70. Aldolase_TIM. 1 hit.
KOK01714.
PANTHERPTHR12128. DHDPS. 1 hit.
PfamPF00701. DHDPS. 1 hit.
[Graphical view]
PIRSFPIRSF001365. DHDPS. 1 hit.
PRINTSPR00146. DHPICSNTHASE.
TIGRFAMsTIGR00674. DapA. 1 hit.
PROSITEPS00665. DHDPS_1. False negative.
PS00666. DHDPS_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDAPA_PORG3
AccessionPrimary (citable) accession number: B2RMB9
Entry history
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: July 1, 2008
Last modified: January 25, 2012
This is version 27 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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