Reviewed, UniProtKB/Swiss-Prot P97084 (COBD_SALTY)

Names and origin

Protein names

Recommended name:
    Threonine-phosphate decarboxylase
    EC=4.1.1.81
Alternative name(s):
    L-threonine-O-3-phosphate decarboxylase

Gene names

Name:	cobD
Ordered Locus Names:	STM0644

Organism

Salmonella typhimurium [Complete proteome] [HAMAP]

Taxonomic identifier

90371 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella

Protein attributes

Sequence length	364 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Decarboxylates L-threonine-O-3-phosphate to yield (R)-1-amino-2-propanol O-2-phosphate, the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin. Ref.1
Catalytic activity	L-threonine O-3-phosphate = (R)-1-aminopropan-2-yl phosphate + CO2.
Cofactor	Pyridoxal phosphate.
Pathway	Cofactor biosynthesis; adenosylcobalamin biosynthesis.
Subunit structure	Homodimer.
Sequence similarities	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.
Mass spectrometry	Molecular mass is 40666 Da from positions 1 - 364. Determined by ESI. Ref.4 Molecular mass is 40894 Da from positions 1 - 364. Determined by ESI. With pyridoxal phosphate. Ref.4

Ontologies

Keywords
Biological process	Cobalamin biosynthesis
Ligand	Pyridoxal phosphate
Molecular function	Lyase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	cobalamin biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro threonine-phosphate decarboxylase activity Inferred from electronic annotation. Source: EC transferase activity, transferring nitrogenous groups Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 364

364

Threonine-phosphate decarboxylase

PRO_0000163822

Amino acid modifications

Modified residue

216

1

N6-(pyridoxal phosphate)lysine

Experimental info

Sequence conflict

6

1

S → T in AAC79515. Ref.1

Sequence conflict

15

1

A → P in AAC79515. Ref.1

Sequence conflict

25

1

Q → H in AAC79515. Ref.1

Sequence conflict

30

1

S → T in AAC79515. Ref.1

Sequence conflict

42 – 45

4

VKRA → LKPP in AAC79515. Ref.1

Secondary structure

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364

Helix Strand Turn

Details...

Beta strand

7 – 9

3

Helix

13 – 19

7

Helix

23 – 25

3

Beta strand

26 – 28

3

Helix

40 – 48

9

Helix

50 – 54

5

Helix

62 – 72

11

Helix

76 – 78

3

Beta strand

79 – 84

6

Helix

85 – 96

12

Beta strand

99 – 106

8

Helix

110 – 117

8

Beta strand

121 – 126

6

Helix

129 – 131

3

Helix

139 – 142

4

Beta strand

149 – 155

7

Turn

157 – 159

3

Helix

165 – 178

14

Beta strand

181 – 185

5

Helix

189 – 191

3

Helix

199 – 201

3

Beta strand

208 – 214

7

Turn

215 – 219

5

Turn

221 – 223

3

Beta strand

226 – 229

4

Helix

233 – 242

10

Helix

250 – 258

9

Helix

259 – 261

3

Helix

263 – 285

23

Beta strand

290 – 292

3

Beta strand

296 – 305

10

Helix

311 – 316

6

Turn

317 – 319

3

Beta strand

335 – 339

5

Helix

343 – 356

14

Sequences

	Sequence		Length	Mass (Da)
	P97084-1 [UniParc]. Last modified July 19, 2003. Version 2. Checksum: B6613FD0AB6D846C	FASTA	364	40,766
	10 20 30 40 50 60 MALFNSAHGG NIREAATVLG ISPDQLLDFS ANINPLGMPV SVKRALIDNL DCIERYPDAD 70 80 90 100 110 120 YFHLHQALAR HHQVPASWIL AGNGETESIF TVASGLKPRR AMIVTPGFAE YGRALAQSGC 130 140 150 160 170 180 EIRRWSLREA DGWQLTDAIL EALTPDLDCL FLCTPNNPTG LLPERPLLQA IADRCKSLNI 190 200 210 220 230 240 NLILDEAFID FIPHETGFIP ALKDNPHIWV LRSLTKFYAI PGLRLGYLVN SDDAAMARMR 250 260 270 280 290 300 RQQMPWSVNA LAALAGEVAL QDSAWQQATW HWLREEGARF YQALCQLPLL TVYPGRANYL 310 320 330 340 350 360 LLRCEREDID LQRRLLTQRI LIRSCANYPG LDSRYYRVAI RSAAQNERLL AALRNVLTGI APAD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"CobD, a novel enzyme with L-threonine-O-3-phosphate decarboxylase activity, is responsible for the synthesis of (R)-1-amino-2-propanol O-2-phosphate, a proposed new intermediate in cobalamin biosynthesis in Salmonella typhimurium LT2." Brushaber K.R., O'Toole G.A., Escalante-Semerena J.C. J. Biol. Chem. 273:2684-2691(1998) [PubMed: 9446573] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION. Strain: LT2.
[2]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Nature 413:852-856(2001) [PubMed: 11677609] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.
[3]	"Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica." Cheong C.-G., Bauer C.B., Brushaber K.R., Escalante-Semerena J.C., Rayment I. Biochemistry 41:4798-4808(2002) [PubMed: 11939774] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[4]	"Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes." Cheong C.-G., Escalante-Semerena J.C., Rayment I. Biochemistry 41:9079-9089(2002) [PubMed: 12119022] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS), MASS SPECTROMETRY.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U90625 Genomic DNA. Translation: AAC79515.1.
AE008725 Genomic DNA. Translation: AAL19595.1.

RefSeq

NP_459636.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1LC5	X-ray	1.46	A	1-364	[»]
1LC7	X-ray	1.80	A	1-364	[»]
1LC8	X-ray	1.80	A	1-364	[»]
1LKC	X-ray	1.80	A	1-364	[»]

ModBase

Search...

Genome annotation databases

GeneID

1252164.

GenomeReviews

Gene locus STM0644 in contig AE006468_GR.

KEGG

stm:STM0644.

NMPDR

fig|99287.1.peg.624.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

P97084.

OMA

P97084. RSFGKFY.

Enzyme and pathway databases

BioCyc

MetaCyc:MON-12856.
STYP99287:STM0644-MON.

BRENDA

4.1.1.81. 2.

Family and domain databases

InterPro

IPR004839. Aminotrans_I/II.
IPR005860. CobD.
IPR004838. NHTrfase_class1_PyrdxlP-BS.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]

Gene3D

G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.

Pfam

PF00155. Aminotran_1_2. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01140. L_thr_O3P_dcar. 1 hit.

PROSITE

PS00105. AA_TRANSFER_CLASS_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

COBD_SALTY

Accession

Primary (citable) accession number: P97084
Secondary accession number(s): Q8ZQZ9

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2003
Last sequence update:	July 19, 2003
Last modified:	June 16, 2009
This is version 67 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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