Q57695 (DAPA_METJA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
4-hydroxy-tetrahydrodipicolinate synthase
Short name=HTPA synthase
EC=4.3.3.7

Gene names

Name:	dapA
Ordered Locus Names:	MJ0244

Organism

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) [Reference proteome] [HAMAP]

Taxonomic identifier

243232 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus › Methanocaldococcus jannaschii

Protein attributes

Sequence length	289 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA) By similarity. HAMAP-Rule MF_00418
Catalytic activity	Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H2O. HAMAP-Rule MF_00418
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. HAMAP-Rule MF_00418
Subunit structure	Homotetramer; dimer of dimers. Ref.2
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the DapA family.
Caution	Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli (PubMed:8993314 and PubMed:20503968) that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB (PubMed:20503968).

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: HAMAP lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4-hydroxy-tetrahydrodipicolinate synthase Inferred from electronic annotation. Source: EC amine-lyase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 289

289

4-hydroxy-tetrahydrodipicolinate synthase HAMAP-Rule MF_00418

PRO_0000103197

Sites

Active site

132

1

Proton donor/acceptor By similarity

Active site

161

1

Schiff-base intermediate with substrate By similarity

Binding site

44

1

Pyruvate By similarity

Binding site

201

1

Pyruvate; via carbonyl oxygen By similarity

Site

43

1

Part of a proton relay during catalysis By similarity

Site

106

1

Part of a proton relay during catalysis By similarity

Secondary structure

1

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289

Helix Strand Turn

Details...

Beta strand

4 – 8

5

Helix

20 – 32

13

Beta strand

36 – 42

7

Turn

43 – 46

4

Helix

47 – 49

3

Helix

52 – 66

15

Beta strand

69 – 75

7

Helix

81 – 94

14

Beta strand

97 – 102

6

Helix

111 – 124

14

Beta strand

129 – 133

5

Helix

135 – 138

4

Helix

144 – 153

10

Beta strand

157 – 162

6

Helix

168 – 176

9

Beta strand

179 – 184

6

Helix

186 – 188

3

Helix

189 – 194

6

Beta strand

199 – 203

5

Helix

204 – 206

3

Helix

209 – 221

13

Helix

224 – 240

17

Beta strand

243 – 245

3

Helix

248 – 256

9

Helix

273 – 285

13

Sequences

	Sequence		Length	Mass (Da)
	Q57695 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 34CD8619C4A53CCA	FASTA	289	31,580
	10 20 30 40 50 60 MFKGVYPAII TPFKNKEVDF DGLEENINFL IENGVSGIVA VGTTGESPTL SHEEHKKVIE 70 80 90 100 110 120 KVVDVVNGRV QVIAGAGSNC TEEAIELSVF AEDVGADAVL SITPYYNKPT QEGLRKHFGK 130 140 150 160 170 180 VAESINLPIV LYNVPSRTAV NLEPKTVKLL AEEYSNISAV KEANPNLSQV SELIHDAKIT 190 200 210 220 230 240 VLSGNDELTL PIIALGGKGV ISVVANIVPK EFVEMVNYAL EGDFEKAREI HYKLFPLMKA 250 260 270 280 MFIETNPIPV KTALNMMGRP AGELRLPLCE MSEEHKKILE NVLKDLGLI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii." Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C. Science 273:1058-1073(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]	"Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii." Padmanabhan B., Strange R.W., Antonyuk S.V., Ellis M.J., Hasnain S.S., Iino H., Agari Y., Bessho Y., Yokoyama S. Acta Crystallogr. F 65:1222-1226(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT. Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L77117 Genomic DNA. Translation: AAB98232.1.

PIR

E64330.

RefSeq

NP_247215.1. NC_000909.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2YXG	X-ray	2.20	A/B/C/D	1-289	[»]

ProteinModelPortal

Q57695.

SMR

Q57695. Positions 1-289.

ModBase

Search...

Protein-protein interaction databases

STRING

243232.MJ0244.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAB98232; AAB98232; MJ_0244.

GeneID

1451098.

KEGG

mja:MJ_0244.

Phylogenomic databases

eggNOG

COG0329.

KO

K01714.

OMA

ADAILCV.

ProtClustDB

PRK03170.

Enzyme and pathway databases

UniPathway

UPA00034; UER00017.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

HAMAP

MF_00418. DapA.

InterPro

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

PANTHER

PTHR12128. PTHR12128. 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...

Other

EvolutionaryTrace

Q57695.

Entry information

Entry name

DAPA_METJA

Accession

Primary (citable) accession number: Q57695

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	May 1, 2013
This is version 82 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program