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BUD16/YEL029C Single Page Format

This page provides an alternative format to the SGD Locus Summary Page. Note that additional information may be available on or linked from the standard format SGD Locus Summary page.

Contents

Names and Identifiers GO Annotations Pathways Summary Paragraph Mutant Phenotypes Interactions Homologs Protein Info (physical properties, transcript info) PDB Homologs (protein structure info) Motifs Genome-wide Expression (and other large-scale analyses) Locus History (misc. notes) Sequence Retrieval and Analysis Map and Displays Localization Community Annotation Literature Guide

Sequence Coordinates   ChrV: 97796 to 96858 CDS: 97796 - 96858 Click on map for expanded view SGD ORF map GBrowse

SGD Locus Page

Names and Identifiers [TOP] [NEXT]
Standard Name	Systematic Name	Alias	Feature Type	SGDID
BUD16	YEL029C		ORF, Verified	S000000755
This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community. Gene name reserved on: 2001-02-13. Gene name expires on 2002-02-13.
Description
Putative pyridoxal kinase, a key enzyme involved in pyridoxal 5'-phosphate synthesis, the active form of vitamin B6; required for genome integrity; involved in bud-site selection; similarity to yeast BUD17 and human pyridoxal kinase (PDXK)

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By ATP binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0067 Assigned on 2007-05-23 UniProtKB kinase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0418 Assigned on 2007-05-23 UniProtKB metal ion binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0479 Assigned on 2007-05-23 UniProtKB nucleotide binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0547 Assigned on 2007-05-23 UniProtKB pyridoxal kinase activity Hanna MC, et al. (1997) Human pyridoxal kinase. cDNA cloning, expression, and modulation by ligands of the benzodiazepine receptor. J Biol Chem 272(16):10756-60        ISA : Inferred from Sequence Alignment with EBI:O00764 Assigned on 2008-12-01 SGD DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR004625 Assigned on 2007-05-23 UniProtKB GOA curators and MGI curators (2001) Gene Ontology annotation based on Enzyme Commission mapping.      IEA : Inferred from Electronic Annotation with IUBMB:2.7.1.35 Assigned on 2008-06-11 UniProtKB transferase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0808 Assigned on 2007-05-23 UniProtKB zinc ion binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0862 Assigned on 2007-05-23 UniProtKB
Biological Process Annotation(s) Reference(s) Evidence Assigned By cell cycle GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0131 Assigned on 2007-05-23 UniProtKB cellular bud site selection Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70        IMP : Inferred from Mutant Phenotype Assigned on 2002-10-10 SGD pyridoxal phosphate biosynthetic process Kanellis P, et al. (2007) A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions. PLoS Genet 3(8):e134          IMP : Inferred from Mutant Phenotype IGI : Inferred from Genetic Interaction with SGD:SNZ1, SGD:SNO1 Assigned on 2008-10-21 SGD pyridoxine biosynthetic process DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR004625 Assigned on 2007-05-23 UniProtKB
Cellular Component Annotation(s) Reference(s) Evidence Assigned By cytoplasm Geraghty MT, et al. (1999) Detecting patterns of protein distribution and gene expression in silico. Proc Natl Acad Sci U S A 96(6):2937-42        IDA : Inferred from Direct Assay Assigned on 2008-12-01 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0963 Assigned on 2008-02-14 UniProtKB GOA curators and UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.      IEA : Inferred from Electronic Annotation with EBI:SL-0086 Assigned on 2008-02-13 UniProtKB nucleus GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0539 Assigned on 2007-05-23 UniProtKB GOA curators and UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.      IEA : Inferred from Electronic Annotation with EBI:SL-0191 Assigned on 2008-02-13 UniProtKB

Pathways [TOP] [NEXT]
pyridoxal 5'-phosphate salvage pathway

Summary Paragraph [TOP] [NEXT]
No summary paragraph available

Basic References [TOP]

BASIC INFORMATION REFERENCES forBUD16/YEL029C for BUD16 1) Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70        2) Hanna MC, et al. (1997) Human pyridoxal kinase. cDNA cloning, expression, and modulation by ligands of the benzodiazepine receptor. J Biol Chem 272(16):10756-60        3) Askree SH, et al. (2004) A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Proc Natl Acad Sci U S A 101(23):8658-63            4) Kanellis P, et al. (2007) A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions. PLoS Genet 3(8):e134

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for BUD16/YEL029C

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for BUD16/YEL029C

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi Candida Homologs (CGD) Candida Homologs (CandidaDB) Fungal Alignment Fungal Orthogroups Repository Ortholog Search (P-POD) PhylomeDB Synteny Viewer Yeast Gene Order Browser (YGOB) eukarYotic OrtholoGY (YOGY)

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations from Predicted Full length Translation N-term MPRLLAT C-term DYIYARL Length(aa) 312 MW(Da) 35,559 pI 6.51 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias 0.027   Codon Adaptation Index 0.140   Frequency of Optimal Codons 0.431   Hydropathicity of Protein -0.141   Aromaticity Score 0.103	10 20 30 40 50 | | | | | MPRLLATQSHVVHGYVGNKAATFPLQCLGWDVDCCNSVQFSNHTGYGLDK VFGTITRETDLKELLSGLFDNFSQDYQALLSGYLPNKNSVRCMGTYYAKF KEANPEMIWLMDPVMGDEGQLYVSEDVIPEYRKLALSPKQLVDIITPNQF ELEILYGGEIKTKEHLKKALKKLHQTIPVIIVTSCDCKMFDDKDFIYCVA SMEGKTPIVYRVPFIDSYFTGVGDLFSALLLDRVYKILSNPTTTLKFEDQ VNNVLNVIQKVLKITRSYASGKMKAKMGSALEMKEMELRLIESRDIYETI NIHQTDYIYARL*

Protein Structures from PDB: proteins of known structure with sequence similarity to BUD16/YEL029C, based on Smith-Waterman analysis. [TOP] [NEXT]

PDB protein structure(s) homologous to BUD16 Homolog Source (per PDB) Protein Alignment: BUD16 vs. Homolog External Links P-Value %Identical %Similar Alignment 1rfu ( Chain: F, E, H, D, A, B, C, G) Crystal structure of pyridoxal kinase complexed with adp and plp PDB_Info PDB_Structure Ovis aries Chain F = 3.1e-35 36 30 View alignment SCOP MMDB CATH Chain E = 3.1e-35 36 30 View alignment Chain H = 3.1e-35 36 30 View alignment Chain D = 3.1e-35 36 30 View alignment Chain A = 3.1e-35 36 30 View alignment Chain B = 3.1e-35 36 30 View alignment Chain C = 3.1e-35 36 30 View alignment Chain G = 3.1e-35 36 30 View alignment 1rfv ( Chain: A, B) Crystal structure of pyridoxal kinase complexed with adp PDB_Info PDB_Structure Ovis aries Chain A = 3.1e-35 36 30 View alignment SCOP MMDB CATH Chain B = 3.1e-35 36 30 View alignment 1ygj ( Chain: A) Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives PDB_Info PDB_Structure Ovis aries 3.1e-35 36 30 View alignment SCOP MMDB CATH 1lhr ( Chain: B, A) Crystal structure of pyridoxal kinase complexed with atp PDB_Info PDB_Structure Ovis aries Chain B = 3.1e-35 36 30 View alignment SCOP MMDB CATH Chain A = 3.1e-35 36 30 View alignment 1lhp ( Chain: B, A) Crystal structure of pyridoxal kinase from sheep brain PDB_Info PDB_Structure Ovis aries Chain B = 3.1e-35 36 30 View alignment SCOP MMDB CATH Chain A = 3.1e-35 36 30 View alignment 1rft ( Chain: A) Crystal structure of pyridoxal kinase complexed with amp- pcp and pyridoxamine PDB_Info PDB_Structure Ovis aries 3.1e-35 36 30 View alignment SCOP MMDB CATH 1yhj ( Chain: A) Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives PDB_Info PDB_Structure Ovis aries 3.1e-35 36 30 View alignment SCOP MMDB CATH 1ygk ( Chain: A) Crystal structure of pyridoxal kinase in complex with roscovitine and derivatives PDB_Info PDB_Structure Ovis aries 3.1e-35 36 30 View alignment SCOP MMDB CATH 2yxu ( Chain: B, A) Human pyridoxal kinase PDB_Info PDB_Structure Homo sapiens Chain B = 6.9e-35 36 31 View alignment SCOP MMDB CATH Chain A = 6.9e-35 36 31 View alignment 2yxt ( Chain: B, A) Human pyridoxal kinase PDB_Info PDB_Structure Homo sapiens Chain B = 6.9e-35 36 31 View alignment SCOP MMDB CATH Chain A = 6.9e-35 36 31 View alignment 2ajp ( Chain: A, B) Crystal structure of a human pyridoxal kinase PDB_Info PDB_Structure Homo sapiens Chain A = 7.3e-35 36 31 View alignment SCOP MMDB CATH Chain B = 7.3e-35 36 31 View alignment 2f7k ( Chain: B, A) Crystal structure of human pyridoxal kinase PDB_Info PDB_Structure Homo sapiens Chain B = 7.3e-35 36 31 View alignment SCOP MMDB CATH Chain A = 7.3e-35 36 31 View alignment 3fhy ( Chain: B, A) Crystal structure of d235n mutant of human pyridoxal kinase PDB_Info PDB_Structure Homo sapiens Chain B = 1.9e-34 36 31 View alignment SCOP MMDB CATH Chain A = 1.9e-34 36 31 View alignment 3fhx ( Chain: B, A) Crystal structure of d235a mutant of human pyridoxal kinase PDB_Info PDB_Structure Homo sapiens Chain B = 3.5e-34 36 31 View alignment SCOP MMDB CATH Chain A = 3.5e-34 36 31 View alignment 1td2 ( Chain: B, A) Crystal structure of the pdxy protein from escherichia coli PDB_Info PDB_Structure Escherichia coli Chain B = 2.3e-16 30 29 View alignment SCOP MMDB CATH Chain A = 2.3e-16 30 29 View alignment 1vi9 ( Chain: B, D, A, C) Crystal structure of pyridoxamine kinase PDB_Info PDB_Structure Escherichia coli Chain B = 2.5e-16 30 29 View alignment SCOP MMDB CATH Chain D = 2.5e-16 30 29 View alignment Chain A = 2.5e-16 30 29 View alignment Chain C = 2.5e-16 30 29 View alignment 2ddo ( Chain: B, A) Crystal structure of pyridoxal kinase from the escherichia coli pdxk gene at 2.6 a resolution PDB_Info PDB_Structure Escherichia coli Chain B = 6.5e-12 28 33 View alignment SCOP MMDB CATH Chain A = 6.5e-12 28 33 View alignment 2ddw ( Chain: A, B) Crystal structure of pyridoxal kinase from the escherichia coli pdxk gene complexed with pyridoxal at 3.2 a resolution PDB_Info PDB_Structure Escherichia coli Chain A = 6.5e-12 28 33 View alignment SCOP MMDB CATH Chain B = 6.5e-12 28 33 View alignment 2ddm ( Chain: B, A) Crystal structure of pyridoxal kinase from the escherichia coli pdxk gene at 2.1 a resolution PDB_Info PDB_Structure Escherichia coli Chain B = 6.5e-12 28 33 View alignment SCOP MMDB CATH Chain A = 6.5e-12 28 33 View alignment 3ibq ( Chain: A) Pyridoxal kinase PDB_Info PDB_Structure Unknown 3.6e-05 24 26 View alignment SCOP MMDB CATH 3hyo ( Chain: A) Pyridoxal kinase PDB_Info PDB_Structure Unknown 3.6e-05 24 26 View alignment SCOP MMDB CATH 3h74 ( Chain: A) Pyridoxal kinase PDB_Info PDB_Structure Unknown 3.6e-05 24 26 View alignment SCOP MMDB CATH 2i5b ( Chain: A, D, B, E, C) The crystal structure of an adp complex of bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution PDB_Info PDB_Structure Bacillus subtilis Chain A = 0.001100 30 25 View alignment SCOP MMDB CATH Chain D = 0.001100 30 25 View alignment Chain B = 0.001100 30 25 View alignment Chain E = 0.001100 30 25 View alignment Chain C = 0.001100 30 25 View alignment

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]
Functional Analysis Expression Connection Summary Cell cycle and metabolic oscillation Cell cycle transcript profile Cyclebase Genevestigator GermOnline SPELL Microarray Search YGAC Triples Yeast Microarray Global Viewer YeastFunc	You can also search multiple datasets simultaneously using Expression Connection for expression studies or Function Junction for other large scale analyses.

Locus History (misc. notes) [TOP] [NEXT]

Nomenclature History

Standard Name	Date Standardized	Reference
BUD16	2001-08-13	Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70

Sequence Retrieval [TOP] [NEXT]
Sequence Type	Output Format
Genomic DNA	GCG | FASTA | NoHeader
Genomic DNA with 1 kb up and downstream	GCG | FASTA | NoHeader
DNA coding sequence (without introns, without flanking regions)	GCG | FASTA | NoHeader
Protein Translation of ORF	GCG | FASTA | NoHeader
6-Frame Translation(with Restriction Map)	GCG
Restriction Fragment Sizes	GCG
Sequence Analysis Tools BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YEL029C	SGD Systematic Sequence
NP_010885.1	NCBI: RefSeq protein version ID
NP_010885.1	NCBI: RefSeq protein version ID
856683	NCBI: Gene ID
6320806	NCBI: NCBI protein GI

Map and Displays [TOP] [NEXT]
Physical, Genetic Maps:	Chromosomal Feature Map	GBrowse	Combined Physical and Genetic Map	Genetic Distance vs. Physical Distance Ratios
Similarity Viewers:	Synteny Viewer	Genomic Stripe View	SAGE Results Map

Localization [TOP] [NEXT]
Localization Resources YeastRC Localization (Seattle) Organelle DB (UMich) YGAC Triples YeastGFP DB (UCSF) at SGD

Community Annotation [TOP] [NEXT]
No community annotation available.

Literature Guide: papers categorized by topic. [TOP]
Topics	Reference	Other Genes Addressed
7 curated references; 0 references not yet curated
Mutants/Phenotypes	Jin YH, et al. (2008) Global transcriptome and deletome profiles of yeast exposed to transition metals. PLoS Genet 4(4):e1000053	|ADH1 |ARN1 |ARN2 |ATM1 |ATX1 |BCK1 |BNI1 |BSD2 |BUD25 |CCC2 |CKA1 |CKA2 |CKB2 |CLN3 |MORE
Function/Process Genetic Interactions Mutants/Phenotypes Non-Fungal Related Genes/Proteins Strains/Constructs	Kanellis P, et al. (2007) A screen for suppressors of gross chromosomal rearrangements identifies a conserved role for PLP in preventing DNA lesions. PLoS Genet 3(8):e134	|ESC2 |MRE11 |RAD18 |RAD27 |RAD5 |RAD52 |RAD6 |RMI1 |RML2 |SGS1 |SLX5 |SLX8 |SNO1 |SNZ1 |MORE
Evolution Fungal Related Genes/Proteins Non-Fungal Related Genes/Proteins	Tanaka T, et al. (2005) Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Mol Biol Evol 22(2):243-50	|BUD17 |PDX3 |SER1 |SNO1 |SNO2 |SNO3 |SNZ1 |SNZ2 |SNZ3 |TDH1 |TDH2 |TDH3
Mutants/Phenotypes Strains/Constructs	Askree SH, et al. (2004) A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Proc Natl Acad Sci U S A 101(23):8658-63	|ADE12 |ADO1 |AGP2 |APE3 |ARG2 |ARV1 |ASC1 |ATG11 |BEM4 |BRE2 |BRO1 |BUD30 |CAX4 |CCW14 |MORE
Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Strains/Constructs	Ni L and Snyder M (2001) A genomic study of the bipolar bud site selection pattern in Saccharomyces cerevisiae. Mol Biol Cell 12(7):2147-70	|ALG8 |BUD13 |BUD14 |BUD17 |BUD19 |BUD20 |BUD21 |BUD22 |BUD23 |BUD25 |BUD26 |BUD27 |BUD28 |BUD30 |MORE
Cellular Location Mutants/Phenotypes Other Features Protein Sequence Features Strains/Constructs	Geraghty MT, et al. (1999) Detecting patterns of protein distribution and gene expression in silico. Proc Natl Acad Sci U S A 96(6):2937-42	|AAT2 |AHP1 |ANT1 |CIT2 |CTA1 |DAL7 |DCI1 |ECI1 |FOX2 |GTO1 |IDP3 |LYS1 |LYS12 |LYS4 |MORE
Non-Fungal Related Genes/Proteins	Hanna MC, et al. (1997) Human pyridoxal kinase. cDNA cloning, expression, and modulation by ligands of the benzodiazepine receptor. J Biol Chem 272(16):10756-60	|BUD17

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