SLYD_ECOLI
ID SLYD_ECOLI Reviewed; 196 AA.
AC P0A9K9; P30856; Q2M714;
DT 19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 19-JUL-2005, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=FKBP-type peptidyl-prolyl cis-trans isomerase SlyD;
DE Short=PPIase;
DE EC=5.2.1.8;
DE AltName: Full=Histidine-rich protein;
DE AltName: Full=Metallochaperone SlyD;
DE AltName: Full=Rotamase;
DE AltName: Full=Sensitivity to lysis protein D;
DE AltName: Full=WHP;
GN Name=slyD; OrderedLocusNames=b3349, JW3311;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-35 AND
RP 141-146.
RC STRAIN=K12 / ATCC 35607 / JM83;
RX PubMed=8300624; DOI=10.1016/s0021-9258(17)42026-6;
RA Wuelfing C., Lomardero J., Plueckthun A.;
RT "An Escherichia coli protein consisting of a domain homologous to FK506-
RT binding proteins (FKBP) and a new metal binding motif.";
RL J. Biol. Chem. 269:2895-2901(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / CS109;
RX PubMed=8300625; DOI=10.1016/s0021-9258(17)42027-8;
RA Roof W.D., Horne S.M., Young K.D., Young R.;
RT "slyD, a host gene required for phi X174 lysis, is related to the FK506-
RT binding protein family of peptidyl-prolyl cis-trans-isomerases.";
RL J. Biol. Chem. 269:2902-2910(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / CS109;
RX PubMed=7540828; DOI=10.1007/bf00404209;
RA Horne S.M., Young K.D.;
RT "Escherichia coli and other species of the Enterobacteriaceae encode a
RT protein similar to the family of Mip-like FK506-binding proteins.";
RL Arch. Microbiol. 163:357-365(1995).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP PROTEIN SEQUENCE OF 1-10, ACTIVITY REGULATION, AND CHARACTERIZATION.
RC STRAIN=BL21;
RX PubMed=9188461; DOI=10.1074/jbc.272.25.15697;
RA Hottenrott S., Schumann T., Plueckthun A., Fischer G., Rahfeld J.-U.;
RT "The Escherichia coli SlyD is a metal ion-regulated peptidyl-prolyl
RT cis/trans-isomerase.";
RL J. Biol. Chem. 272:15697-15701(1997).
RN [7]
RP FUNCTION IN LYSIS OF PHIX174 INFECTED CELLS.
RX PubMed=12100551; DOI=10.1046/j.1365-2958.2002.02984.x;
RA Bernhardt T.G., Roof W.D., Young R.;
RT "The Escherichia coli FKBP-type PPIase SlyD is required for the
RT stabilization of the E lysis protein of bacteriophage phi X174.";
RL Mol. Microbiol. 45:99-108(2002).
RN [8]
RP FUNCTION IN HYDROGENASE METALLOCENTER ASSEMBLY, AND INTERACTION WITH HYPB.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=15569666; DOI=10.1074/jbc.m411799200;
RA Zhang J.W., Butland G., Greenblatt J.F., Emili A., Zamble D.B.;
RT "A role for SlyD in the Escherichia coli hydrogenase biosynthetic
RT pathway.";
RL J. Biol. Chem. 280:4360-4366(2005).
RN [9]
RP FUNCTION AS A CHAPERONE AND A PPIASE, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, AND DOMAIN.
RX PubMed=16388577; DOI=10.1021/bi051922n;
RA Scholz C., Eckert B., Hagn F., Schaarschmidt P., Balbach J., Schmid F.X.;
RT "SlyD proteins from different species exhibit high prolyl isomerase and
RT chaperone activities.";
RL Biochemistry 45:20-33(2006).
RN [10]
RP FUNCTION IN HYDROGENASE METALLOCENTER ASSEMBLY, DOMAIN, AND MUTAGENESIS OF
RP ILE-42 AND PHE-132.
RX PubMed=17720786; DOI=10.1128/jb.00922-07;
RA Zhang J.W., Leach M.R., Zamble D.B.;
RT "The peptidyl-prolyl isomerase activity of SlyD is not required for
RT maturation of Escherichia coli hydrogenase.";
RL J. Bacteriol. 189:7942-7944(2007).
RN [11]
RP FUNCTION, AND INTERACTION WITH TAT SIGNAL SEQUENCES.
RC STRAIN=K12 / MC4100 / JA176;
RX PubMed=17215254; DOI=10.1074/jbc.m608235200;
RA Graubner W., Schierhorn A., Bruser T.;
RT "DnaK plays a pivotal role in Tat targeting of CueO and functions beside
RT SlyD as a general Tat signal binding chaperone.";
RL J. Biol. Chem. 282:7116-7124(2007).
RN [12]
RP SUBUNIT, NICKEL-BINDING, DOMAIN, AND MUTAGENESIS OF 167-CYS-CYS-168 AND
RP 184-CYS-CYS-185.
RX PubMed=19947632; DOI=10.1021/ja9081765;
RA Kaluarachchi H., Sutherland D.E., Young A., Pickering I.J., Stillman M.J.,
RA Zamble D.B.;
RT "The Ni(II)-binding properties of the metallochaperone SlyD.";
RL J. Am. Chem. Soc. 131:18489-18500(2009).
RN [13]
RP STRUCTURE BY NMR, NICKEL-BINDING, AND DOMAIN.
RX PubMed=19645725; DOI=10.1111/j.1742-4658.2009.07159.x;
RA Martino L., He Y., Hands-Taylor K.L., Valentine E.R., Kelly G.,
RA Giancola C., Conte M.R.;
RT "The interaction of the Escherichia coli protein SlyD with nickel ions
RT illuminates the mechanism of regulation of its peptidyl-prolyl isomerase
RT activity.";
RL FEBS J. 276:4529-4544(2009).
RN [14]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=22412352; DOI=10.1371/journal.pbio.1001281;
RA Erental A., Sharon I., Engelberg-Kulka H.;
RT "Two programmed cell death systems in Escherichia coli: an apoptotic-like
RT death is inhibited by the mazEF-mediated death pathway.";
RL PLoS Biol. 10:E1001281-E1001281(2012).
RN [15]
RP STRUCTURE BY NMR OF 1-165, FUNCTION AS A CHAPERONE, DOMAIN, AND BINDING TO
RP UNFOLDED PROTEINS.
RX PubMed=19356587; DOI=10.1016/j.jmb.2009.01.034;
RA Weininger U., Haupt C., Schweimer K., Graubner W., Kovermann M., Bruser T.,
RA Scholz C., Schaarschmidt P., Zoldak G., Schmid F.X., Balbach J.;
RT "NMR solution structure of SlyD from Escherichia coli: spatial separation
RT of prolyl isomerase and chaperone function.";
RL J. Mol. Biol. 387:295-305(2009).
CC -!- FUNCTION: Folding helper with both chaperone and peptidyl-prolyl cis-
CC trans isomerase (PPIase) activities. Chaperone activity prevents
CC aggregation of unfolded or partially folded proteins and promotes their
CC correct folding. PPIases catalyze the cis-trans isomerization of Xaa-
CC Pro bonds of peptides, which accelerates slow steps of protein folding
CC and thus shortens the lifetime of intermediates. Both strategies lower
CC the concentration of intermediates and increase the productivity and
CC yield of the folding reaction. SlyD could be involved in Tat-dependent
CC translocation, by binding to the Tat-type signal of folded proteins.
CC The PPIase substrate specificity, carried out with synthetic peptides
CC of the 'suc-Ala-Xaa-Pro-Phe-4NA' type (where Xaa is the AA tested), was
CC found to be Phe > Ala > Leu.
CC -!- FUNCTION: Required for lysis of phiX174 infected cells by stabilizing
CC the hydrophobic viral lysis protein E and allowing it to accumulate to
CC the levels required to exert its lytic effect. May act by a chaperone-
CC like mechanism.
CC -!- FUNCTION: Also involved in hydrogenase metallocenter assembly, probably
CC by participating in the nickel insertion step. This function in
CC hydrogenase biosynthesis requires chaperone activity and the presence
CC of the metal-binding domain, but not PPIase activity.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=[protein]-peptidylproline (omega=180) = [protein]-
CC peptidylproline (omega=0); Xref=Rhea:RHEA:16237, Rhea:RHEA-
CC COMP:10747, Rhea:RHEA-COMP:10748, ChEBI:CHEBI:83833,
CC ChEBI:CHEBI:83834; EC=5.2.1.8;
CC Evidence={ECO:0000269|PubMed:16388577};
CC -!- ACTIVITY REGULATION: PPIase activity is inhibited by binding of nickel
CC ions to the C-terminal metal-binding region and/or the C-terminal part
CC of the PPIase domain. Folding activity is inhibited by FK506 and by
CC permanently unfolded proteins, irrespective of their proline content.
CC {ECO:0000269|PubMed:16388577, ECO:0000269|PubMed:9188461}.
CC -!- SUBUNIT: Monomer. Binds to a broad range of unrelated Tat signal
CC sequences. Interacts with the hydrogenase nickel incorporation protein
CC HypB. {ECO:0000269|PubMed:15569666, ECO:0000269|PubMed:17215254,
CC ECO:0000269|PubMed:19947632}.
CC -!- INTERACTION:
CC P0A9K9; P68066: grcA; NbExp=3; IntAct=EBI-369251, EBI-561424;
CC P0A9K9; P16431: hycE; NbExp=7; IntAct=EBI-369251, EBI-552702;
CC P0A9K9; P0AAN3: hypB; NbExp=6; IntAct=EBI-369251, EBI-558261;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- DOMAIN: The N-terminal region consists of two globular folded domains
CC that contain prolyl isomerase and chaperone activities.
CC -!- DOMAIN: The C-terminal region binds up to 7 nickel ions in a non-
CC cooperative manner. Can also bind zinc with high affinity, and copper
CC or cobalt with lower affinity. No binding detectable for ferrous,
CC ferric, magnesium and calcium ions. Binding of nickel causes
CC conformational rearrangements in the PPIase domain, modulating its
CC isomerase activity. This region is also important for hydrogenase
CC biosynthesis.
CC -!- DISRUPTION PHENOTYPE: Cells undergo an apoptotic-like death upon DNA
CC damage characterized by membrane depolarization.
CC {ECO:0000269|PubMed:22412352}.
CC -!- MISCELLANEOUS: The activity of SlyD is considerably smaller than the
CC one found in other PPIases with the same substrate.
CC -!- SIMILARITY: Belongs to the FKBP-type PPIase family. {ECO:0000305}.
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DR EMBL; Z21496; CAA79705.1; -; Genomic_DNA.
DR EMBL; L13261; AAA18574.1; -; Unassigned_DNA.
DR EMBL; L28082; AAC41458.1; -; Genomic_DNA.
DR EMBL; U18997; AAA58146.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76374.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77942.1; -; Genomic_DNA.
DR PIR; A49987; A49987.
DR RefSeq; NP_417808.1; NC_000913.3.
DR RefSeq; WP_000861334.1; NZ_STEB01000004.1.
DR PDB; 2K8I; NMR; -; A=1-165.
DR PDB; 2KFW; NMR; -; A=1-196.
DR PDB; 5I7P; X-ray; 2.00 A; A=70-129.
DR PDBsum; 2K8I; -.
DR PDBsum; 2KFW; -.
DR PDBsum; 5I7P; -.
DR AlphaFoldDB; P0A9K9; -.
DR BMRB; P0A9K9; -.
DR SMR; P0A9K9; -.
DR BioGRID; 4260682; 44.
DR DIP; DIP-31853N; -.
DR IntAct; P0A9K9; 124.
DR MINT; P0A9K9; -.
DR STRING; 511145.b3349; -.
DR jPOST; P0A9K9; -.
DR PaxDb; P0A9K9; -.
DR PRIDE; P0A9K9; -.
DR EnsemblBacteria; AAC76374; AAC76374; b3349.
DR EnsemblBacteria; BAE77942; BAE77942; BAE77942.
DR GeneID; 66672771; -.
DR GeneID; 947859; -.
DR KEGG; ecj:JW3311; -.
DR KEGG; eco:b3349; -.
DR PATRIC; fig|511145.12.peg.3442; -.
DR EchoBASE; EB1614; -.
DR eggNOG; COG1047; Bacteria.
DR HOGENOM; CLU_098197_1_0_6; -.
DR InParanoid; P0A9K9; -.
DR OMA; HSHEGGC; -.
DR PhylomeDB; P0A9K9; -.
DR BioCyc; EcoCyc:EG11663-MON; -.
DR BioCyc; MetaCyc:EG11663-MON; -.
DR EvolutionaryTrace; P0A9K9; -.
DR PRO; PR:P0A9K9; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0050897; F:cobalt ion binding; IDA:EcoCyc.
DR GO; GO:0005507; F:copper ion binding; IDA:EcoCyc.
DR GO; GO:0016151; F:nickel cation binding; IDA:EcoCyc.
DR GO; GO:0003755; F:peptidyl-prolyl cis-trans isomerase activity; IDA:EcoCyc.
DR GO; GO:0051082; F:unfolded protein binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0043963; P:modulation by symbiont of host adenylate cyclase-mediated signal transduction; IMP:UniProtKB.
DR GO; GO:0051604; P:protein maturation; IMP:EcoCyc.
DR GO; GO:0022417; P:protein maturation by protein folding; IMP:EcoliWiki.
DR GO; GO:0000413; P:protein peptidyl-prolyl isomerization; IDA:EcoCyc.
DR GO; GO:0042026; P:protein refolding; IDA:EcoCyc.
DR GO; GO:0050821; P:protein stabilization; IMP:EcoliWiki.
DR GO; GO:0009408; P:response to heat; IEP:EcoliWiki.
DR DisProt; DP00766; -.
DR Gene3D; 3.10.50.40; -; 1.
DR InterPro; IPR046357; PPIase_dom_sf.
DR InterPro; IPR001179; PPIase_FKBP_dom.
DR Pfam; PF00254; FKBP_C; 1.
DR PROSITE; PS50059; FKBP_PPIASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chaperone; Cobalt; Copper; Cytoplasm;
KW Direct protein sequencing; Isomerase; Metal-binding; Nickel;
KW Reference proteome; Rotamase; Zinc.
FT CHAIN 1..196
FT /note="FKBP-type peptidyl-prolyl cis-trans isomerase SlyD"
FT /id="PRO_0000075355"
FT DOMAIN 1..95
FT /note="PPIase FKBP-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00277"
FT REGION 1..69
FT /note="PPIase first part"
FT REGION 76..120
FT /note="IF-chaperone"
FT REGION 129..151
FT /note="PPIase second part"
FT BINDING 167
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000255"
FT BINDING 168
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000255"
FT BINDING 184
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000255"
FT BINDING 185
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000255"
FT BINDING 193
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000255"
FT BINDING 195
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000255"
FT MUTAGEN 42
FT /note="I->S: Decrease in PPIase activity, but has little
FT impact on chaperone activity and interaction with HypB.
FT Almost complete loss of PPIase activity; when associated
FT with Y-132."
FT /evidence="ECO:0000269|PubMed:17720786"
FT MUTAGEN 132
FT /note="F->Y: Almost complete loss of PPIase activity, but
FT has little impact on chaperone activity and interaction
FT with HypB; when associated with S-42."
FT /evidence="ECO:0000269|PubMed:17720786"
FT MUTAGEN 167..168
FT /note="CC->AA: Reduces nickel-binding capacity."
FT /evidence="ECO:0000269|PubMed:19947632"
FT MUTAGEN 184..185
FT /note="CC->AA: Reduces nickel-binding capacity."
FT /evidence="ECO:0000269|PubMed:19947632"
FT STRAND 7..17
FT /evidence="ECO:0007829|PDB:2K8I"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:2KFW"
FT STRAND 22..25
FT /evidence="ECO:0007829|PDB:2K8I"
FT STRAND 28..30
FT /evidence="ECO:0007829|PDB:2K8I"
FT STRAND 32..35
FT /evidence="ECO:0007829|PDB:2K8I"
FT HELIX 44..49
FT /evidence="ECO:0007829|PDB:2K8I"
FT STRAND 50..52
FT /evidence="ECO:0007829|PDB:2KFW"
FT STRAND 57..63
FT /evidence="ECO:0007829|PDB:2K8I"
FT TURN 64..66
FT /evidence="ECO:0007829|PDB:2K8I"
FT STRAND 67..69
FT /evidence="ECO:0007829|PDB:2KFW"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:5I7P"
FT STRAND 76..79
FT /evidence="ECO:0007829|PDB:5I7P"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:5I7P"
FT STRAND 95..100
FT /evidence="ECO:0007829|PDB:5I7P"
FT STRAND 103..112
FT /evidence="ECO:0007829|PDB:5I7P"
FT STRAND 117..120
FT /evidence="ECO:0007829|PDB:5I7P"
FT TURN 124..127
FT /evidence="ECO:0007829|PDB:5I7P"
FT STRAND 130..139
FT /evidence="ECO:0007829|PDB:5I7P"
FT HELIX 145..148
FT /evidence="ECO:0007829|PDB:2K8I"
FT STRAND 177..182
FT /evidence="ECO:0007829|PDB:2KFW"
SQ SEQUENCE 196 AA; 20853 MW; 46DCC7C7ECD61DBA CRC64;
MKVAKDLVVS LAYQVRTEDG VLVDESPVSA PLDYLHGHGS LISGLETALE GHEVGDKFDV
AVGANDAYGQ YDENLVQRVP KDVFMGVDEL QVGMRFLAET DQGPVPVEIT AVEDDHVVVD
GNHMLAGQNL KFNVEVVAIR EATEEELAHG HVHGAHDHHH DHDHDGCCGG HGHDHGHEHG
GEGCCGGKGN GGCGCH
