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Entry version 58 (13 Feb 2019)
Sequence version 1 (16 Dec 2008)
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Protein

Riboflavin biosynthesis protein PYRD, chloroplastic

Gene

PYRD

Organism
Zea mays (Maize)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at transcript leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Monofunctional pyrimidine deaminase involved in the riboflavin biosynthesis pathway. Has also a reductase domain that lacks catalytically essential substrate-binding residues (By similarity).By similarity

Miscellaneous

Unlike bacteria that have a bifunctional, two-domain RibD enzyme, plants have a monofunctional reductase and a monofunctional deaminase, each having an enzymatically inactive domain.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Zn2+By similarityNote: Binds 1 zinc ion.By similarity

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: riboflavin biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Riboflavin biosynthesis protein PYRD, chloroplastic (PYRD)
  3. Riboflavin biosynthesis protein PYRR, chloroplastic (PYRR)
  4. no protein annotated in this organism
This subpathway is part of the pathway riboflavin biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi95Zinc; catalyticBy similarity1
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei97Proton donorBy similarity1
Metal bindingi120Zinc; catalyticBy similarity1
Metal bindingi129Zinc; catalyticBy similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionHydrolase
LigandMetal-binding

Enzyme and pathway databases

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00275;UER00401

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Riboflavin biosynthesis protein PYRD, chloroplastic
Including the following 2 domains:
Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC:3.5.4.26)
Short name:
DRAP deaminase
Alternative name(s):
Riboflavin-specific deaminase
Inactive 5-amino-6-(5-phosphoribosylamino)uracil reductase
Alternative name(s):
HTP reductase
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:PYRD
ORF Names:GRMZM2G320099Curated
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiZea mays (Maize)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri4577 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaePACMAD cladePanicoideaeAndropogonodaeAndropogoneaeTripsacinaeZea
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000007305 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Unplaced

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chloroplast, Plastid

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a transit peptide.<p><a href='/help/transit' target='_top'>More...</a></p>Transit peptidei1 – 26ChloroplastSequence analysisAdd BLAST26
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_000042270527 – 392Riboflavin biosynthesis protein PYRD, chloroplasticAdd BLAST366

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
B6TRH4

PRoteomics IDEntifications database

More...
PRIDEi
B6TRH4

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
4577.GRMZM2G320099_P01

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
B6TRH4

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
B6TRH4

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini46 – 168CMP/dCMP-type deaminasePROSITE-ProRule annotationAdd BLAST123

Keywords - Domaini

Transit peptide

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG410IU3W Eukaryota
COG0117 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000257443

KEGG Orthology (KO)

More...
KOi
K11752

Database of Orthologous Groups

More...
OrthoDBi
619775at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.430.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR016192 APOBEC/CMP_deaminase_Zn-bd
IPR002125 CMP_dCMP_dom
IPR016193 Cytidine_deaminase-like
IPR024072 DHFR-like_dom_sf
IPR004794 Eubact_RibD

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00383 dCMP_cyt_deam_1, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF006769 RibD, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF53597 SSF53597, 1 hit
SSF53927 SSF53927, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00326 eubact_ribD, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00903 CYT_DCMP_DEAMINASES_1, 1 hit
PS51747 CYT_DCMP_DEAMINASES_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

B6TRH4-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MASSLVSRPH LTQRPVRAAT LASATRPRLA AGALSGRCQA QAAGDLDDAH
60 70 80 90 100
YMRRCVELAR KAAGHTSPNP MVGCVIVRDG RVVGEGFHPK AGQPHAEVFA
110 120 130 140 150
LRDAGNLAEN ATAYVSLEPC NHYGRTPPCT EALINAKVKE VVVGMTDPNP
160 170 180 190 200
IVASKGIEKL QGAGISVRVG VEEALCRKLN EAYIHRMLTG KAFATLRATL
210 220 230 240 250
SMNGIITNQI GKGADQSGGY YSQLMKEYDG VIISSDLAKM SALPLSREAG
260 270 280 290 300
TNQPLCIIIA QGESSRLHIP SLSQEHASRA IVLADSPVTV EPAGVEVAVF
310 320 330 340 350
RQIDLESILQ LLAQRGLCSV LVDFREAGES FASLLNDFQE DKLVQKVVVE
360 370 380 390
VLPFWLASDG LSNLAFGGSQ SFPLKNLELR DVNGSVLLEG YV
Length:392
Mass (Da):41,834
Last modified:December 16, 2008 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iDD0BA3B63267DDE4
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti30A → V in ACF78978 (PubMed:19936069).Curated1
Sequence conflicti35S → G in ACF78978 (PubMed:19936069).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
EU967589 mRNA Translation: ACG39707.1
BT033973 mRNA Translation: ACF78978.1

NCBI Reference Sequences

More...
RefSeqi
NP_001130669.1, NM_001137197.1

UniGene gene-oriented nucleotide sequence clusters

More...
UniGenei
Zm.34641

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
100191772

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
zma:100191772

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU967589 mRNA Translation: ACG39707.1
BT033973 mRNA Translation: ACF78978.1
RefSeqiNP_001130669.1, NM_001137197.1
UniGeneiZm.34641

3D structure databases

ProteinModelPortaliB6TRH4
SMRiB6TRH4
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi4577.GRMZM2G320099_P01

Proteomic databases

PaxDbiB6TRH4
PRIDEiB6TRH4

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100191772
KEGGizma:100191772

Phylogenomic databases

eggNOGiENOG410IU3W Eukaryota
COG0117 LUCA
HOGENOMiHOG000257443
KOiK11752
OrthoDBi619775at2759

Enzyme and pathway databases

UniPathwayi
UPA00275;UER00401

Family and domain databases

Gene3Di3.40.430.10, 1 hit
InterProiView protein in InterPro
IPR016192 APOBEC/CMP_deaminase_Zn-bd
IPR002125 CMP_dCMP_dom
IPR016193 Cytidine_deaminase-like
IPR024072 DHFR-like_dom_sf
IPR004794 Eubact_RibD
PfamiView protein in Pfam
PF00383 dCMP_cyt_deam_1, 1 hit
PIRSFiPIRSF006769 RibD, 1 hit
SUPFAMiSSF53597 SSF53597, 1 hit
SSF53927 SSF53927, 1 hit
TIGRFAMsiTIGR00326 eubact_ribD, 1 hit
PROSITEiView protein in PROSITE
PS00903 CYT_DCMP_DEAMINASES_1, 1 hit
PS51747 CYT_DCMP_DEAMINASES_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRIBD_MAIZE
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: B6TRH4
Secondary accession number(s): B4FA35
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 26, 2013
Last sequence update: December 16, 2008
Last modified: February 13, 2019
This is version 58 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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