Reviewed, UniProtKB/Swiss-Prot P0A544 (SERA_MYCTU)

Names and origin

Protein names

Recommended name:
    D-3-phosphoglycerate dehydrogenase
      Short name=PGDH
    EC=1.1.1.95

Gene names

Name:	serA
Ordered Locus Names:	Rv2996c, MT3074
ORF Names:	MTV012.10

Organism

Mycobacterium tuberculosis [Complete proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	528 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH. 2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.
Pathway	Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glyceric acid: step 1/3.
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. Contains 1 ACT domain.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Serine biosynthesis
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	L-serine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	NAD or NADH binding Inferred from electronic annotation. Source: InterPro amino acid binding Inferred from electronic annotation. Source: InterPro phosphoglycerate dehydrogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 528

528

D-3-phosphoglycerate dehydrogenase

PRO_0000076005

Regions

Domain

454 – 525

72

ACT

Sites

Active site

232

1

By similarity

Active site

261

1

By similarity

Active site

279

1

Proton donor By similarity

Secondary structure

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528

Helix Strand Turn

Details...

Beta strand

5 – 8

4

Helix

14 – 17

4

Beta strand

22 – 28

7

Helix

34 – 40

7

Helix

41 – 43

3

Beta strand

45 – 49

5

Beta strand

51 – 53

3

Helix

57 – 61

5

Beta strand

68 – 74

7

Helix

81 – 86

6

Beta strand

90 – 92

3

Helix

99 – 114

16

Helix

117 – 125

9

Helix

131 – 133

3

Beta strand

143 – 147

5

Helix

151 – 161

11

Turn

162 – 164

3

Beta strand

166 – 170

5

Helix

176 – 182

7

Helix

189 – 195

7

Beta strand

197 – 201

5

Turn

207 – 211

5

Helix

215 – 218

4

Beta strand

226 – 229

4

Helix

238 – 246

9

Beta strand

248 – 250

3

Beta strand

252 – 257

6

Beta strand

259 – 262

4

Helix

267 – 270

4

Beta strand

274 – 276

3

Helix

285 – 303

19

Turn

321 – 325

5

Helix

326 – 339

14

Beta strand

341 – 343

3

Beta strand

346 – 354

9

Helix

355 – 358

4

Helix

362 – 372

11

Helix

374 – 376

3

Helix

386 – 393

8

Beta strand

396 – 403

8

Beta strand

406 – 417

12

Beta strand

423 – 431

9

Turn

432 – 435

4

Beta strand

436 – 442

7

Beta strand

445 – 451

7

Beta strand

453 – 461

9

Helix

466 – 476

11

Beta strand

481 – 488

8

Beta strand

490 – 493

4

Beta strand

495 – 503

9

Helix

507 – 517

11

Beta strand

519 – 526

8

Sequences

	Sequence		Length	Mass (Da)
	P0A544-1 [UniParc]. Last modified March 15, 2005. Version 1. Checksum: 3B5696AAFD82A901	FASTA	528	54,554
	10 20 30 40 50 60 MSLPVVLIAD KLAPSTVAAL GDQVEVRWVD GPDRDKLLAA VPEADALLVR SATTVDAEVL 70 80 90 100 110 120 AAAPKLKIVA RAGVGLDNVD VDAATARGVL VVNAPTSNIH SAAEHALALL LAASRQIPAA 130 140 150 160 170 180 DASLREHTWK RSSFSGTEIF GKTVGVVGLG RIGQLVAQRI AAFGAYVVAY DPYVSPARAA 190 200 210 220 230 240 QLGIELLSLD DLLARADFIS VHLPKTPETA GLIDKEALAK TKPGVIIVNA ARGGLVDEAA 250 260 270 280 290 300 LADAITGGHV RAAGLDVFAT EPCTDSPLFE LAQVVVTPHL GASTAEAQDR AGTDVAESVR 310 320 330 340 350 360 LALAGEFVPD AVNVGGGVVN EEVAPWLDLV RKLGVLAGVL SDELPVSLSV QVRGELAAEE 370 380 390 400 410 420 VEVLRLSALR GLFSAVIEDA VTFVNAPALA AERGVTAEIC KASESPNHRS VVDVRAVGAD 430 440 450 460 470 480 GSVVTVSGTL YGPQLSQKIV QINGRHFDLR AQGINLIIHY VDRPGALGKI GTLLGTAGVN 490 500 510 520 IQAAQLSEDA EGPGATILLR LDQDVPDDVR TAIAAAVDAY KLEVVDLS

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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

BX842581 Genomic DNA. Translation: CAE55535.1.
AE000516 Genomic DNA. Translation: AAK47403.1.

PIR

G70854.

RefSeq

NP_337589.1.
YP_177916.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1YGY	X-ray	2.30	A/B	2-528	[»]
3DC2	X-ray	2.70	A/B	2-528	[»]
3DDN	X-ray	2.40	A/B	2-528	[»]

ModBase

Search...

Genome annotation databases

GeneID

887154.
925199.

GenomeReviews

Gene locus MT3074 in contig AE000516_GR.
Gene locus Rv2996c in contig AL123456_GR.

KEGG

mtc:MT3074.
mtu:Rv2996c.

TIGR

MT3074.

Organism-specific databases

TubercuList

Rv2996c.

Phylogenomic databases

HOGENOM

P0A544.

OMA

P0A544. DMPGIIG.

Enzyme and pathway databases

BRENDA

1.1.1.95. 809.

Family and domain databases

InterPro

IPR002912. ACT_bd.
IPR006236. D-3-Phosphoglycerate_DH.
IPR006139. D-isomer_2_OHA_DH.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR015508. D3PG_DH.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

PANTHER

PTHR10996:SF20. D3PG_Deh. 1 hit.

Pfam

PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF01842. ACT. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01327. PGDH. 1 hit.

PROSITE

PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

SERA_MYCTU

Accession

Primary (citable) accession number: P0A544
Secondary accession number(s): O53243

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 15, 2005
Last sequence update:	March 15, 2005
Last modified:	June 16, 2009
This is version 35 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)