P63945 (DAPA_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Dihydrodipicolinate synthase
Short name=DHDPS
EC=4.2.1.52

Gene names

Name:	dapA
Ordered Locus Names:	Rv2753c, MT2823
ORF Names:	MTV002.18c

Organism

Mycobacterium tuberculosis

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

Bacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	300 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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.
Miscellaneous	Was identified as a high-confidence drug target. HAMAP MF_00418
Sequence similarities	Belongs to the DHDPS family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Diaminopimelate biosynthesis Lysine biosynthesis
Cellular component	Cytoplasm
Ligand	Schiff base
Molecular function	Lyase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	diaminopimelate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW growth Inferred from mutant phenotype. Source: MTBBASE protein homotetramerization Inferred from physical interaction. Source: MTBBASE
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell plasma membrane Inferred from direct assay. Source: MTBBASE
Molecular function	dihydrodipicolinate synthase activity Inferred from direct assay. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 300

300

Dihydrodipicolinate synthase HAMAP MF_00418

PRO_0000103128

Regions

Region

58 – 59

2

Pyruvate binding By similarity

Sites

Active site

171

1

Schiff-base intermediate with substrate By similarity

Binding site

116

1

Pyruvate By similarity

Site

143

1

Involved in proton transfer during cleavage By similarity

Secondary structure

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300

Helix Strand Turn

Details...

Helix

8 – 12

5

Beta strand

14 – 18

5

Helix

31 – 43

13

Beta strand

47 – 53

7

Turn

54 – 60

7

Helix

63 – 77

15

Turn

78 – 80

3

Beta strand

81 – 86

6

Helix

92 – 105

14

Beta strand

108 – 113

6

Helix

122 – 133

12

Beta strand

140 – 144

5

Helix

146 – 149

4

Helix

155 – 162

8

Beta strand

167 – 172

6

Helix

177 – 187

11

Beta strand

190 – 193

4

Helix

196 – 198

3

Helix

199 – 205

7

Beta strand

209 – 213

5

Helix

215 – 230

16

Helix

234 – 254

21

Helix

256 – 266

11

Helix

283 – 295

13

Sequences

	Sequence		Length	Mass (Da)
	P63945 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 71CB322661416367	FASTA	300	30,858
	10 20 30 40 50 60 MTTVGFDVAA RLGTLLTAMV TPFSGDGSLD TATAARLANH LVDQGCDGLV VSGTTGESPT 70 80 90 100 110 120 TTDGEKIELL RAVLEAVGDR ARVIAGAGTY DTAHSIRLAK ACAAEGAHGL LVVTPYYSKP 130 140 150 160 170 180 PQRGLQAHFT AVADATELPM LLYDIPGRSA VPIEPDTIRA LASHPNIVGV KDAKADLHSG 190 200 210 220 230 240 AQIMADTGLA YYSGDDALNL PWLAMGATGF ISVIAHLAAG QLRELLSAFG SGDIATARKI 250 260 270 280 290 300 NIAVAPLCNA MSRLGGVTLS KAGLRLQGID VGDPRLPQVA ATPEQIDALA ADMRAASVLR

References

[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G. Nature 393:537-544(1998) [PubMed: 9634230] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed: 12218036] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis." Raman K., Yeturu K., Chandra N. BMC Syst. Biol. 2:109-109(2008) [PubMed: 19099550] [Abstract] Cited for: IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BX842580 Genomic DNA. Translation: CAA15549.1.
AE000516 Genomic DNA. Translation: AAK47142.1.

PIR

H70879.

RefSeq

NP_217269.1. NC_000962.2.
NP_337328.1. NC_002755.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1XXX	X-ray	2.28	A/B/C/D/E/F/G/H	2-300	[»]
3L21	X-ray	2.10	A/B/C/D/E/F	2-300	[»]

ProteinModelPortal

P63945.

SMR

P63945. Positions 5-300.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBMYCT00000000449; EBMYCP00000000449; EBMYCG00000000449.
EBMYCT00000071768; EBMYCP00000069827; EBMYCG00000071763.

GeneID

888289.
925466.

GenomeReviews

Gene locus MT2823 in contig AE000516_GR.
Gene locus Rv2753c in contig AL123456_GR.

KEGG

mtc:MT2823.
mtu:Rv2753c.

PATRIC

18127960. VBIMycTub22151_3079.

TIGR

MT2823.

Organism-specific databases

TubercuList

Rv2753c.

Phylogenomic databases

GeneTree

EBGT00050000016215.

HOGENOM

HBG358848.

OMA

HGCISVV.

PhylomeDB

P63945.

ProtClustDB

PRK03170.

Family and domain databases

HAMAP

MF_00418. DapA.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR002220. Dihydrodipicolinate_synth-like.
IPR020625. Dihydrodipicolinate_synth_AS.
IPR020624. Dihydrodipicolinate_synth_CS.
IPR005263. Dihydrodipicolinate_synth_DapA.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.

KO

K01714.

PANTHER

PTHR12128. DHDPS. 1 hit.

Pfam

PF00701. DHDPS. 1 hit.
[Graphical view]

PIRSF

PIRSF001365. DHDPS. 1 hit.

PRINTS

PR00146. DHPICSNTHASE.

TIGRFAMs

TIGR00674. DapA. 1 hit.

PROSITE

PS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

DAPA_MYCTU

Accession

Primary (citable) accession number: P63945
Secondary accession number(s): O33295

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	January 25, 2012
This is version 54 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program