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Q1CIM4

- PDXH_YERPN

UniProt

Q1CIM4 - PDXH_YERPN

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Protein
Pyridoxine/pyridoxamine 5'-phosphate oxidase
Gene
pdxH, YPN_1827, YP516_2029
Organism
Yersinia pestis bv. Antiqua (strain Nepal516)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP) By similarity.UniRule annotation

Catalytic activityi

Pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH3 + H2O2.UniRule annotation
Pyridoxine 5'-phosphate + O2 = pyridoxal 5'-phosphate + H2O2.UniRule annotation

Cofactori

Binds 1 FMN per subunit By similarity.UniRule annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei66 – 661FMN By similarity
Binding sitei69 – 691FMN; via amide nitrogen By similarity
Binding sitei71 – 711Substrate By similarity
Binding sitei88 – 881FMN By similarity
Binding sitei128 – 1281Substrate By similarity
Binding sitei132 – 1321Substrate By similarity
Binding sitei136 – 1361Substrate By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi81 – 822FMN By similarity
Nucleotide bindingi145 – 1462FMN By similarity

GO - Molecular functioni

  1. FMN binding Source: UniProtKB-HAMAP
  2. pyridoxamine-phosphate oxidase activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. pyridoxine biosynthetic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Flavoprotein, FMN

Enzyme and pathway databases

BioCyciYPES377628:GIXK-1886-MONOMER.
UniPathwayiUPA00190; UER00304.
UPA00190; UER00305.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine/pyridoxamine 5'-phosphate oxidase (EC:1.4.3.5)
Alternative name(s):
PNP/PMP oxidase
Short name:
PNPOx
Pyridoxal 5'-phosphate synthase
Gene namesi
Name:pdxH
Ordered Locus Names:YPN_1827
ORF Names:YP516_2029
OrganismiYersinia pestis bv. Antiqua (strain Nepal516)
Taxonomic identifieri377628 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeYersinia
ProteomesiUP000008936: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 217217Pyridoxine/pyridoxamine 5'-phosphate oxidaseUniRule annotation
PRO_0000255898Add
BLAST

Interactioni

Subunit structurei

Homodimer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi377628.YPN_1827.

Structurei

3D structure databases

ProteinModelPortaliQ1CIM4.
SMRiQ1CIM4. Positions 9-217.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni13 – 164Substrate binding By similarity
Regioni196 – 1983Substrate binding By similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0259.
HOGENOMiHOG000242755.
KOiK00275.
OrthoDBiEOG60KN2Z.

Family and domain databases

Gene3Di2.30.110.10. 1 hit.
HAMAPiMF_01629. PdxH.
InterProiIPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view]
PANTHERiPTHR10851. PTHR10851. 1 hit.
PfamiPF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view]
PIRSFiPIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMiSSF50475. SSF50475. 1 hit.
TIGRFAMsiTIGR00558. pdxH. 1 hit.
PROSITEiPS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q1CIM4-1 [UniParc]FASTAAdd to Basket

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MTENNEFDVA DLRREYIRGG LRRSDLTENP LELFERWLKQ ACEARLPDPT    50
AMCVATVDTN GQPYQRIVLL KHYDDQGLVF YTNLGSRKAQ QLAENPHISL 100
LFPWHMLDRQ VIFLGKAERL STLEVLKYFH SRPKDSQIGA WVSQQSSRIS 150
ARGVLESKFL ELKQKFQQGD VPLPSFWGGF RVKFDSVEFW QGGEHRLHDR 200
FIYQREADAW KIDRLAP 217
Length:217
Mass (Da):25,383
Last modified:October 31, 2006 - v2
Checksum:i0CB7B6F07CB1DA86
GO

Sequence cautioni

The sequence ABG18156.1 differs from that shown. Reason: Erroneous initiation.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000305 Genomic DNA. Translation: ABG18156.1. Different initiation.
ACNQ01000010 Genomic DNA. Translation: EEO76729.1.
RefSeqiYP_647756.2. NC_008149.1.

Genome annotation databases

EnsemblBacteriaiABG18156; ABG18156; YPN_1827.
EEO76729; EEO76729; YP516_2029.
GeneIDi4125695.
KEGGiypn:YPN_1827.
PATRICi18603102. VBIYerPes46733_2212.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000305 Genomic DNA. Translation: ABG18156.1 . Different initiation.
ACNQ01000010 Genomic DNA. Translation: EEO76729.1 .
RefSeqi YP_647756.2. NC_008149.1.

3D structure databases

ProteinModelPortali Q1CIM4.
SMRi Q1CIM4. Positions 9-217.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 377628.YPN_1827.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABG18156 ; ABG18156 ; YPN_1827 .
EEO76729 ; EEO76729 ; YP516_2029 .
GeneIDi 4125695.
KEGGi ypn:YPN_1827.
PATRICi 18603102. VBIYerPes46733_2212.

Phylogenomic databases

eggNOGi COG0259.
HOGENOMi HOG000242755.
KOi K00275.
OrthoDBi EOG60KN2Z.

Enzyme and pathway databases

UniPathwayi UPA00190 ; UER00304 .
UPA00190 ; UER00305 .
BioCyci YPES377628:GIXK-1886-MONOMER.

Family and domain databases

Gene3Di 2.30.110.10. 1 hit.
HAMAPi MF_01629. PdxH.
InterProi IPR000659. Pyridox_Oxase.
IPR019740. Pyridox_Oxase_CS.
IPR011576. Pyridox_Oxase_FMN-bd.
IPR019576. Pyridoxamine_oxidase_dimer_C.
IPR012349. Split_barrel_FMN-bd.
[Graphical view ]
PANTHERi PTHR10851. PTHR10851. 1 hit.
Pfami PF10590. PNPOx_C. 1 hit.
PF01243. Pyridox_oxidase. 1 hit.
[Graphical view ]
PIRSFi PIRSF000190. Pyd_amn-ph_oxd. 1 hit.
SUPFAMi SSF50475. SSF50475. 1 hit.
TIGRFAMsi TIGR00558. pdxH. 1 hit.
PROSITEi PS01064. PYRIDOX_OXIDASE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen."
    Chain P.S.G., Hu P., Malfatti S.A., Radnedge L., Larimer F., Vergez L.M., Worsham P., Chu M.C., Andersen G.L.
    J. Bacteriol. 188:4453-4463(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Nepal516.
  2. "Yersinia pestis Nepal516A whole genome shotgun sequencing project."
    Plunkett G. III, Anderson B.D., Baumler D.J., Burland V., Cabot E.L., Glasner J.D., Mau B., Neeno-Eckwall E., Perna N.T., Munk A.C., Tapia R., Green L.D., Rogers Y.C., Detter J.C., Bruce D.C., Brettin T.S.
    Submitted (APR-2009) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiPDXH_YERPN
AccessioniPrimary (citable) accession number: Q1CIM4
Secondary accession number(s): C4GTC8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: October 31, 2006
Last modified: May 14, 2014
This is version 64 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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