DERK_MYCS2
ID DERK_MYCS2 Reviewed; 580 AA.
AC A0QXE4;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=D-erythrulose kinase {ECO:0000303|PubMed:26560079};
DE EC=2.7.1.210 {ECO:0000269|PubMed:26560079};
GN Name=derK {ECO:0000303|PubMed:26560079};
GN OrderedLocusNames=MSMEG_3271 {ECO:0000312|EMBL:ABK70898.1},
GN MSMEI_3187 {ECO:0000312|EMBL:AFP39650.1};
OS Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium
OS smegmatis).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=246196;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RA Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
RA Fraser C.M.;
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
RA Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
RA Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
RT "Interrupted coding sequences in Mycobacterium smegmatis: authentic
RT mutations or sequencing errors?";
RL Genome Biol. 8:R20.1-R20.9(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=18955433; DOI=10.1101/gr.081901.108;
RA Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
RA Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
RT "Ortho-proteogenomics: multiple proteomes investigation through orthology
RT and a new MS-based protocol.";
RL Genome Res. 19:128-135(2009).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, INDUCTION, DISRUPTION PHENOTYPE, AND PATHWAY.
RC STRAIN=ATCC 700084 / mc(2)155;
RX PubMed=26560079; DOI=10.1021/jacs.5b08968;
RA Huang H., Carter M.S., Vetting M.W., Al-Obaidi N., Patskovsky Y.,
RA Almo S.C., Gerlt J.A.;
RT "A general strategy for the discovery of metabolic pathways: D-threitol, L-
RT threitol, and erythritol utilization in Mycobacterium smegmatis.";
RL J. Am. Chem. Soc. 137:14570-14573(2015).
CC -!- FUNCTION: Catalyzes the phosphorylation of D-erythrulose to D-
CC erythrulose-4P. Involved in the degradation pathways of erythritol and
CC D-threitol, that allow M.smegmatis to grow on these compounds as the
CC sole carbon source. {ECO:0000269|PubMed:26560079}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + D-erythrulose = ADP + D-erythrulose 4-phosphate + H(+);
CC Xref=Rhea:RHEA:48768, ChEBI:CHEBI:15378, ChEBI:CHEBI:16023,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:90796, ChEBI:CHEBI:456216;
CC EC=2.7.1.210; Evidence={ECO:0000269|PubMed:26560079};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.6 uM for D-erythrulose {ECO:0000269|PubMed:26560079};
CC KM=396 uM for L-erythrulose {ECO:0000269|PubMed:26560079};
CC KM=339 uM for dihydroxyacetone {ECO:0000269|PubMed:26560079};
CC Note=kcat is 2.88 sec(-1) with D-erythrulose as substrate. kcat is
CC 0.091 sec(-1) with L-erythrulose as substrate. kcat is 0.063 sec(-1)
CC with dihydroxyacetone as substrate. {ECO:0000269|PubMed:26560079};
CC -!- PATHWAY: Carbohydrate metabolism; erythritol degradation.
CC {ECO:0000269|PubMed:26560079}.
CC -!- PATHWAY: Carbohydrate metabolism; D-threitol degradation.
CC {ECO:0000269|PubMed:26560079}.
CC -!- INDUCTION: Up-regulated during growth on erythritol, D-threitol or L-
CC threitol relative to growth on glycerol. {ECO:0000269|PubMed:26560079}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are defective for growth
CC with D-threitol and are totally unable to grow on erythritol.
CC {ECO:0000269|PubMed:26560079}.
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DR EMBL; CP000480; ABK70898.1; -; Genomic_DNA.
DR EMBL; CP001663; AFP39650.1; -; Genomic_DNA.
DR RefSeq; WP_011728941.1; NZ_SIJM01000015.1.
DR RefSeq; YP_887582.1; NC_008596.1.
DR AlphaFoldDB; A0QXE4; -.
DR SMR; A0QXE4; -.
DR STRING; 246196.MSMEI_3187; -.
DR PRIDE; A0QXE4; -.
DR EnsemblBacteria; ABK70898; ABK70898; MSMEG_3271.
DR EnsemblBacteria; AFP39650; AFP39650; MSMEI_3187.
DR GeneID; 66734671; -.
DR KEGG; msg:MSMEI_3187; -.
DR KEGG; msm:MSMEG_3271; -.
DR PATRIC; fig|246196.19.peg.3232; -.
DR eggNOG; COG2376; Bacteria.
DR OMA; TALNMNG; -.
DR OrthoDB; 857242at2; -.
DR BioCyc; MetaCyc:MON-19890; -.
DR BRENDA; 2.7.1.210; 3512.
DR UniPathway; UPA01065; -.
DR UniPathway; UPA01066; -.
DR Proteomes; UP000000757; Chromosome.
DR Proteomes; UP000006158; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0030246; F:carbohydrate binding; IDA:UniProtKB.
DR GO; GO:0019200; F:carbohydrate kinase activity; IDA:UniProtKB.
DR GO; GO:0004371; F:glycerone kinase activity; IEA:InterPro.
DR GO; GO:0016052; P:carbohydrate catabolic process; IMP:UniProtKB.
DR GO; GO:0009758; P:carbohydrate utilization; IMP:UniProtKB.
DR GO; GO:0071322; P:cellular response to carbohydrate stimulus; IDA:UniProtKB.
DR GO; GO:0006071; P:glycerol metabolic process; IEA:InterPro.
DR Gene3D; 1.25.40.340; -; 1.
DR InterPro; IPR004006; DhaK_dom.
DR InterPro; IPR004007; DhaL_dom.
DR InterPro; IPR036117; DhaL_dom_sf.
DR Pfam; PF02733; Dak1; 1.
DR Pfam; PF02734; Dak2; 1.
DR SMART; SM01120; Dak2; 1.
DR SUPFAM; SSF101473; SSF101473; 1.
DR PROSITE; PS51481; DHAK; 1.
DR PROSITE; PS51480; DHAL; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Carbohydrate metabolism; Kinase; Nucleotide-binding;
KW Reference proteome; Transferase.
FT CHAIN 1..580
FT /note="D-erythrulose kinase"
FT /id="PRO_0000435515"
FT DOMAIN 7..327
FT /note="DhaK"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00814"
FT DOMAIN 368..570
FT /note="DhaL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00813"
FT REGION 329..360
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 217
FT /note="Tele-hemiaminal-histidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P76015"
FT BINDING 397..403
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P76014"
FT BINDING 443..444
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P76014"
FT BINDING 485
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P76014"
FT BINDING 542
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P76014"
FT BINDING 555..557
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P76014"
SQ SEQUENCE 580 AA; 59699 MW; 418C44867C921CC1 CRC64;
MTKLFNDPAR FTEDMLVGFL DANSRYVVGV PGGVVRAQTT RPGKVAVVIG GGSGHYPAFC
GTVGPGFADG AVVGNIFTSP SAEEAASVAR AAHSDAGVLL TTGNYAGDVM NFNLAVDQLR
SEGIEAQYFA VTDDVASAER GQEAKRRGIA GDFTVFKCAS AAAEEGLDLA GVVRVAEAAN
AATRTLGVAF DGCTLPGADH PLFTVPEGHM GLGLGIHGEP GVSEEKMPTA AGLAATLVDG
VLGDRPDAPE KRIAVILNGL GRTKYEELFV VWGEVSRLLR DRGYTIVEPE VGELVTSLDM
AGCSLTVMWL DEELERYWAA PADTPAYKKG AAQQHVSGER RSEATARSAS SGPKLAELSD
EDGRAGARLV ARAFDAMAEA LADAEEELGR IDAVAGDGDH GRGMVKGSSA AREAAASALS
EGAGQGSVLN AAGKAWAAKA GGTSGVLWGA LLTALGARLG DTGRPDSSVI AAGVRDAYDA
LIRLGGAAPG DKTMLDAMLP FTEELERRVA QDESWQSAWR AAADVATEAA RATADLRPKI
GRARPLAERS VGTPDAGATS LALCARTVAD CVTLSTQGEN
