Q5L3Y2 (PDXS_GEOKA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pyridoxal biosynthesis lyase pdxS
EC=4.-.-.-

Gene names

Name:	pdxS
Ordered Locus Names:	GK0011

Organism

Geobacillus kaustophilus (strain HTA426) [Complete proteome] [HAMAP]

Taxonomic identifier

235909 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	294 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in the production of pyridoxal phosphate, probably by incorporating ammonia into the pyridine ring By similarity. HAMAP MF_01824
Pathway	Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis. HAMAP MF_01824
Subunit structure	Forms a complex with pdxT By similarity. HAMAP MF_01824
Sequence similarities	Belongs to the pdxS/SNZ family.

Ontologies

Keywords
Ligand	Pyridoxal phosphate
Molecular function	Lyase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	pyridoxal phosphate biosynthetic process Inferred from electronic annotation. Source: InterPro
Molecular function	lyase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 294

294

Pyridoxal biosynthesis lyase pdxS HAMAP MF_01824

PRO_0000109395

Secondary structure

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294

Helix Strand Turn

Details...

Beta strand

20 – 27

8

Helix

28 – 36

9

Beta strand

40 – 44

5

Helix

64 – 73

10

Beta strand

78 – 83

6

Helix

87 – 95

9

Beta strand

99 – 104

6

Helix

118 – 120

3

Beta strand

125 – 131

7

Helix

132 – 140

9

Beta strand

144 – 148

5

Helix

158 – 176

19

Helix

179 – 181

3

Helix

182 – 189

8

Helix

193 – 202

10

Beta strand

209 – 214

6

Helix

218 – 226

9

Beta strand

230 – 234

5

Helix

237 – 240

4

Beta strand

241 – 243

3

Helix

244 – 256

13

Turn

257 – 259

3

Helix

261 – 268

8

Sequences

	Sequence		Length	Mass (Da)
	Q5L3Y2 [UniParc]. Last modified February 1, 2005. Version 1. Checksum: 3427A52A7DE63F50	FASTA	294	31,652
	10 20 30 40 50 60 MALTGTDRVK RGMAEMQKGG VIMDVVNAEQ AKIAEAAGAV AVMALERVPA DIRAAGGVAR 70 80 90 100 110 120 MADPTVIEEV MNAVSIPVMA KVRIGHYVEA RVLEALGVDY IDESEVLTPA DEEFHIDKRQ 130 140 150 160 170 180 FTVPFVCGCR DLGEAARRIA EGASMLRTKG EPGTGNIVEA VRHMRKVNAQ IRKVVNMSED 190 200 210 220 230 240 ELVAEAKQLG APVEVLREIK RLGRLPVVNF AAGGVATPAD AALMMHLGAD GVFVGSGIFK 250 260 270 280 290 SENPEKYARA IVEATTHYED YELIAHLSKG LGGAMRGIDI ATLLPEHRMQ ERGW

References

[1]	"Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus." Takami H., Takaki Y., Chee G.-J., Nishi S., Shimamura S., Suzuki H., Matsui S., Uchiyama I. Nucleic Acids Res. 32:6292-6303(2004) [PubMed: 15576355] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: HTA426.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000043 Genomic DNA. Translation: BAD74296.1.

RefSeq

YP_145864.1. NC_006510.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZNN	X-ray	2.20	A/B/C/D/E/F	1-294	[»]

ProteinModelPortal

Q5L3Y2.

SMR

Q5L3Y2. Positions 18-271.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

3185318.

GenomeReviews

Gene locus GK0011 in contig BA000043_GR.

KEGG

gka:GK0011.

NMPDR

fig|235909.3.peg.112.

PATRIC

21961027. VBIGeoKau81518_0056.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG292342.

OMA

RIWEGAA.

ProtClustDB

PRK04180.

Enzyme and pathway databases

BioCyc

GKAU235909:GK0011-MONOMER.

Family and domain databases

HAMAP

MF_01824. PdxS.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR011060. RibuloseP-bd_barrel.
IPR001852. Snz1p/Sor1.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 2 hits.

KO

K06215.

PANTHER

PTHR22854:SF9. PTHR22854:SF9. 1 hit.

Pfam

PF01680. SOR_SNZ. 1 hit.
[Graphical view]

PIRSF

PIRSF029271. Pdx1. 1 hit.

SUPFAM

SSF51366. RibP_bind_barrel. 1 hit.

TIGRFAMs

TIGR00343. TIGR00343. 1 hit.

PROSITE

PS01235. PDXS_SNZ_1. 1 hit.
PS51129. PDXS_SNZ_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PDXS_GEOKA

Accession

Primary (citable) accession number: Q5L3Y2

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2005
Last sequence update:	February 1, 2005
Last modified:	January 25, 2012
This is version 50 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program