O59080 (PDXS_PYRHO) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Gene names

Name:	pdxS
Ordered Locus Names:	PH1355

Organism

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) [Complete proteome] [HAMAP]

Taxonomic identifier

70601 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus › Pyrococcus horikoshii

Protein attributes

Sequence length	335 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-Rule MF_01824
Pathway	Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis. HAMAP-Rule MF_01824
Subunit structure	Forms a complex with PdxT By similarity.
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: HAMAP
Molecular_function	2-iminoacetate synthase activity 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 – 335

335

Pyridoxal biosynthesis lyase PdxS HAMAP-Rule MF_01824

PRO_0000109445

Secondary structure

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335

Helix Strand Turn

Details...

Helix

3 – 21

19

Turn

22 – 25

4

Beta strand

26 – 33

8

Helix

34 – 43

10

Beta strand

46 – 50

5

Helix

55 – 60

6

Helix

70 – 77

8

Beta strand

84 – 89

6

Helix

93 – 102

10

Beta strand

105 – 113

9

Helix

124 – 126

3

Beta strand

131 – 137

7

Helix

138 – 147

10

Beta strand

150 – 154

5

Helix

164 – 181

18

Helix

185 – 195

11

Helix

197 – 200

4

Helix

201 – 209

9

Beta strand

221 – 223

3

Helix

228 – 245

18

Beta strand

249 – 254

6

Helix

261 – 269

9

Beta strand

273 – 277

5

Helix

279 – 282

4

Beta strand

283 – 285

3

Helix

287 – 299

13

Turn

300 – 302

3

Helix

304 – 312

9

Sequences

	Sequence		Length	Mass (Da)
	O59080 [UniParc]. Last modified August 1, 1998. Version 1. Checksum: D5E178BB654E5196	FASTA	335	37,014
	10 20 30 40 50 60 MDKLKIIMEK GTERLKRGFA KMVKGGVIMD VTNAEQARIA EEAGAVAVMA LHKVPADIRK 70 80 90 100 110 120 AGGVARMAPV EKIQEIMDAV TIPVMAKCRI GHEAEARILE ALGVDMIDES EVLTPADPFF 130 140 150 160 170 180 HIYKKKFTAP FVCGARNLGE AVRRIWEGAA MIRTKGEAGT GNIIEAVRHV RLVNENIRLI 190 200 210 220 230 240 QRMTDEEIYG VAEKFAEPYL RLAFSVKEIS GLPKRVLENE PIYEGFTYRE IVEDIYKILL 250 260 270 280 290 300 EIKKLGRLPV VNFAAGGVAT PADAALMMAM GMDGVFVGSG IFKSSNPPKM ARAIVEAVNH 310 320 330 WDEPDVLAEI SREIGEPMRG QAIEELQVRM EERGI

References

[1]

"Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3." Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K., Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T. , Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T., Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H. DNA Res. 5:55-76(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.

+

Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000001 Genomic DNA. Translation: BAA30461.1.

PIR

E71007.

RefSeq

NP_143237.1. NC_000961.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4FIQ	X-ray	2.70	A/B/C/D/E/F	1-335	[»]
4FIR	X-ray	3.10	A/B/C/D/E/F	1-335	[»]

ProteinModelPortal

O59080.

SMR

O59080. Positions 12-320.

ModBase

Search...

Protein-protein interaction databases

MINT

MINT-1501312.

STRING

70601.PH1355.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

BAA30461; BAA30461; BAA30461.

GeneID

1443680.

KEGG

pho:PH1355.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG0214.

HOGENOM

HOG000227586.

KO

K06215.

OMA

ARMSDPD.

ProtClustDB

PRK04180.

Enzyme and pathway databases

BioCyc

PHOR70601:GJWR-1361-MONOMER.

UniPathway

UPA00245.

Family and domain databases

Gene3D

3.20.20.70. 2 hits.

HAMAP

MF_01824. PdxS.

InterPro

IPR013785. Aldolase_TIM.
IPR011060. RibuloseP-bd_barrel.
IPR001852. Snz1p/Sor1.
IPR008867. ThiG.
[Graphical view]

Pfam

PF01680. SOR_SNZ. 1 hit.
PF05690. ThiG. 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_PYRHO

Accession

Primary (citable) accession number: O59080

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 13, 2004
Last sequence update:	August 1, 1998
Last modified:	May 1, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program