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Protein

3-methyl-2-oxobutanoate hydroxymethyltransferase

Gene

panB

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible reaction in which hydroxymethyl group from 5,10-methylenetetrahydrofolate is tranferred onto alpha-ketoisovalerate to form ketopantoate.1 Publication

Catalytic activityi

5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = tetrahydrofolate + 2-dehydropantoate.1 Publication

Cofactori

Mg2+2 Publications, Co2+2 Publications, Zn2+2 Publications, Ni2+2 Publications, Ca2+2 PublicationsNote: Binds 1 Mg2+ ion per subunit. Can also use Co2+, Zn2+, Ni2+ and Ca2+ to a lesser extent.2 Publications

Kineticsi

  1. KM=240 µM for alpha-ketoisovalerate (at 37 degrees Celsius and pH 7.5)1 Publication
  2. KM=820 µM for 5,10-methylenetetrahydrofolate (at 37 degrees Celsius and pH 7.5)1 Publication
  1. Vmax=1.6 µmol/min/mg enzyme (at 37 degrees Celsius and pH 7.5)1 Publication

pH dependencei

Optimum pH is 7.0-7.5.1 Publication

Pathwayi: (R)-pantothenate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes (R)-pantoate from 3-methyl-2-oxobutanoate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB), 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB)
  2. 2-dehydropantoate 2-reductase (LH57_14090), Putative 2-dehydropantoate 2-reductase (Rv2573)
This subpathway is part of the pathway (R)-pantothenate 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 (R)-pantoate from 3-methyl-2-oxobutanoate, the pathway (R)-pantothenate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi62 – 621Magnesium
Metal bindingi101 – 1011MagnesiumBy similarity
Binding sitei101 – 1011Alpha-ketoisovalerateBy similarity
Binding sitei131 – 1311Alpha-ketoisovalerateBy similarity
Metal bindingi133 – 1331Magnesium
Active sitei199 – 1991Proton acceptorBy similarity

GO - Molecular functioni

  • 3-methyl-2-oxobutanoate hydroxymethyltransferase activity Source: MTBBASE
  • magnesium ion binding Source: MTBBASE

GO - Biological processi

  • growth Source: MTBBASE
  • pantothenate biosynthetic process Source: MTBBASE
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pantothenate biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00028; UER00003.

Names & Taxonomyi

Protein namesi
Recommended name:
3-methyl-2-oxobutanoate hydroxymethyltransferase (EC:2.1.2.11)
Alternative name(s):
Ketopantoate hydroxymethyltransferase
Short name:
KPHMT
Gene namesi
Name:panB
Ordered Locus Names:Rv2225
ORF Names:MTCY427.06
OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Taxonomic identifieri83332 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001584 Componenti: Chromosome

Organism-specific databases

TubercuListiRv2225.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • plasma membrane Source: MTBBASE
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedCombined sources1 Publication
Chaini2 – 2812803-methyl-2-oxobutanoate hydroxymethyltransferasePRO_0000184864Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineCombined sources

Post-translational modificationi

Pupylated at an undetermined lysine residue by the prokaryotic ubiquitin-like protein Pup with the help of the ligase PafA, which leads to its degradation by the proteasome. The cross-link involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a lysine in PanB.1 Publication

Keywords - PTMi

Acetylation, Ubl conjugation

Proteomic databases

PaxDbiP9WIL7.

Interactioni

Subunit structurei

Homodecamer; pentamer of dimers.1 Publication

Protein-protein interaction databases

STRINGi83332.Rv2225.

Structurei

Secondary structure

1
281
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi23 – 3210Combined sources
Beta strandi36 – 405Combined sources
Helixi44 – 518Combined sources
Turni52 – 543Combined sources
Beta strandi57 – 604Combined sources
Helixi64 – 674Combined sources
Beta strandi72 – 765Combined sources
Helixi79 – 813Combined sources
Helixi83 – 9210Combined sources
Beta strandi96 – 1016Combined sources
Helixi111 – 12313Combined sources
Beta strandi128 – 1358Combined sources
Helixi136 – 1383Combined sources
Helixi139 – 14810Combined sources
Beta strandi152 – 1576Combined sources
Helixi176 – 19116Combined sources
Beta strandi194 – 2007Combined sources
Helixi203 – 21210Combined sources
Beta strandi217 – 2226Combined sources
Beta strandi226 – 2316Combined sources
Helixi233 – 2364Combined sources
Helixi254 – 27017Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OY0X-ray2.80A/B/C/D/E1-281[»]
ProteinModelPortaliP9WIL7.
SMRiP9WIL7. Positions 18-279.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni62 – 632Alpha-ketoisovalerate bindingBy similarity

Sequence similaritiesi

Belongs to the PanB family.Curated

Phylogenomic databases

eggNOGiENOG4105CCG. Bacteria.
COG0413. LUCA.
KOiK00606.
OMAiDMLGFFD.
PhylomeDBiP9WIL7.

Family and domain databases

CDDicd06557. KPHMT-like. 1 hit.
Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_00156. PanB. 1 hit.
InterProiIPR003700. Pantoate_hydroxy_MeTrfase.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PANTHERiPTHR20881. PTHR20881. 1 hit.
PfamiPF02548. Pantoate_transf. 1 hit.
[Graphical view]
PIRSFiPIRSF000388. Pantoate_hydroxy_MeTrfase. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR00222. panB. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P9WIL7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEQTIYGAN TPGGSGPRTK IRTHHLQRWK ADGHKWAMLT AYDYSTARIF
60 70 80 90 100
DEAGIPVLLV GDSAANVVYG YDTTVPISID ELIPLVRGVV RGAPHALVVA
110 120 130 140 150
DLPFGSYEAG PTAALAAATR FLKDGGAHAV KLEGGERVAE QIACLTAAGI
160 170 180 190 200
PVMAHIGFTP QSVNTLGGFR VQGRGDAAEQ TIADAIAVAE AGAFAVVMEM
210 220 230 240 250
VPAELATQIT GKLTIPTVGI GAGPNCDGQV LVWQDMAGFS GAKTARFVKR
260 270 280
YADVGGELRR AAMQYAQEVA GGVFPADEHS F
Length:281
Mass (Da):29,336
Last modified:April 16, 2014 - v1
Checksum:iE05CDDC5B7E80932
GO

Mass spectrometryi

Molecular mass is 29202 Da from positions 2 - 281. Determined by ESI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA. Translation: CCP45003.1.
PIRiE70776.
RefSeqiNP_216741.1. NC_000962.3.
WP_003411489.1. NZ_KK339370.1.

Genome annotation databases

EnsemblBacteriaiCCP45003; CCP45003; Rv2225.
GeneIDi887440.
KEGGimtu:Rv2225.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA. Translation: CCP45003.1.
PIRiE70776.
RefSeqiNP_216741.1. NC_000962.3.
WP_003411489.1. NZ_KK339370.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1OY0X-ray2.80A/B/C/D/E1-281[»]
ProteinModelPortaliP9WIL7.
SMRiP9WIL7. Positions 18-279.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv2225.

Proteomic databases

PaxDbiP9WIL7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCP45003; CCP45003; Rv2225.
GeneIDi887440.
KEGGimtu:Rv2225.

Organism-specific databases

TubercuListiRv2225.

Phylogenomic databases

eggNOGiENOG4105CCG. Bacteria.
COG0413. LUCA.
KOiK00606.
OMAiDMLGFFD.
PhylomeDBiP9WIL7.

Enzyme and pathway databases

UniPathwayiUPA00028; UER00003.

Family and domain databases

CDDicd06557. KPHMT-like. 1 hit.
Gene3Di3.20.20.60. 1 hit.
HAMAPiMF_00156. PanB. 1 hit.
InterProiIPR003700. Pantoate_hydroxy_MeTrfase.
IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
[Graphical view]
PANTHERiPTHR20881. PTHR20881. 1 hit.
PfamiPF02548. Pantoate_transf. 1 hit.
[Graphical view]
PIRSFiPIRSF000388. Pantoate_hydroxy_MeTrfase. 1 hit.
SUPFAMiSSF51621. SSF51621. 1 hit.
TIGRFAMsiTIGR00222. panB. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPANB_MYCTU
AccessioniPrimary (citable) accession number: P9WIL7
Secondary accession number(s): L0TAJ8, P0A5Q8, Q10505
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: September 7, 2016
This is version 18 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Was identified as a natural substrate of the M.tuberculosis proteasome.
Was identified as a high-confidence drug target.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.