RegulonDB RegulonDB 11.1: Gene Form
   

surA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

lptD surA pdxA rsmA TSS_109 TSS_109 TSS_108 (cluster) TSS_108 (cluster) TSS_107 TSS_107 TSS_106 TSS_106 TSS_105 TSS_105 TSS_104 TSS_104 TSS_103 (cluster) TSS_103 (cluster) TSS_102 (cluster) TSS_102 (cluster) TSS_101 TSS_101 TSS_100 TSS_100 TSS_99 TSS_99 TSS_98 TSS_98 TSS_97 TSS_97 TSS_96 (cluster) TSS_96 (cluster) TSS_95 TSS_95 TSS_94 TSS_94 TSS_93 TSS_93 TSS_92 TSS_92 TSS_91 TSS_91 TSS_90 TSS_90 rsmAp rsmAp TSS_89 TSS_89 TSS_88 TSS_88 TSS_87 (cluster) TSS_87 (cluster) TSS_86 TSS_86 apaGp apaGp TSS_84 TSS_84

Gene      
Name: surA    Texpresso search in the literature
Synonym(s): ECK0054, EG10985, b0053
Genome position(nucleotides): 53416 <-- 54702
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.85
External database links:  
ASAP:
 ABE-0000180
CGSC:
 30326
ECHOBASE:
 EB0978
ECOLIHUB:
 surA
OU-MICROARRAY:
 b0053
STRING:
 511145.b0053
COLOMBOS: surA


Product      
Name: chaperone SurA
Synonym(s): SurA
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 47.284
Isoelectric point: 6.985
Motif(s):
 
Type Positions Sequence Comment
1 -> 20 MKNWKTLLLGIAMIANTSFA
21 -> 428 APQVVDKVAAVVNNGVVLESDVDGLMQSVKLNAAQARQQLPDDATLRHQIMERLIMDQIILQMGQKMGVKISDEQLDQAIANIAKQNNMTLDQMRSRLAYDGLNYNTYRNQIRKEMIISEVRNNEVRRRITILPQEVESLAQQVGNQNDASTELNLSHILIPLPENPTSDQVNEAESQARAIVDQARNGADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGESKNISVTEVHARHILLKPSPIMTDEQARVKLEQIAADIKSGKTTFAAAAKEFSQDPGSANQGGDLGWATPDIFDPAFRDALTRLNKGQMSAPVHSSFGWHLIELLDTRNVDKTDAAQKDRAYRMLMNRKFSEEAASWMQEQRASAYVKILSN UniProt: Chaperone SurA.
25 -> 25 V UniProt: In Ref. 1..
116 -> 116 S UniProt: In Ref. 1..
171 -> 272 STELNLSHILIPLPENPTSDQVNEAESQARAIVDQARNGADFGKLAIAHSADQQALNGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVND UniProt: PpiC 1.

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0005515 - protein binding
GO:0016853 - isomerase activity
GO:0051082 - unfolded protein binding
GO:0003755 - peptidyl-prolyl cis-trans isomerase activity
GO:0042277 - peptide binding
biological_process GO:0006457 - protein folding
GO:0050821 - protein stabilization
GO:0043165 - Gram-negative-bacterium-type cell outer membrane assembly
GO:0060274 - maintenance of stationary phase
GO:0061077 - chaperone-mediated protein folding
GO:0000413 - protein peptidyl-prolyl isomerization
GO:0036506 - maintenance of unfolded protein
Note(s): Note(s): ...[more].
Reference(s): [1] Ades SE., et al., 1999
[2] Bothmann H., et al., 2000
[3] Chai Q., et al., 2014
[4] Cook GM., et al., 1997
[5] Costello SM., et al., 2016
[6] Dartigalongue C., et al., 2001
[7] Geitner AJ., et al., 2013
[8] Jia M., et al., 2019
[9] Jia M., et al., 2020
[10] Jin F. 2020
[11] Ma HW., et al., 2004
[12] Marx DC., et al., 2020
[13] Mogensen JE., et al., 2005
[14] O'Reilly EK., et al., 2004
[15] Pease AJ., et al., 2002
[16] Rouviere PE., et al., 1995
[17] Rudd KE., et al., 1995
[18] Schiffrin B., et al., 2017
[19] Vulic M., et al., 2002
[20] Werner J., et al., 2003
[21] Werner J., et al., 2005
[22] Wu S., et al., 2011
[23] Zhong M., et al., 2013
External database links:  
ALPHAFOLD:
 P0ABZ6
DIP:
 DIP-35827N
ECOCYC:
 EG10985-MONOMER
ECOLIWIKI:
 b0053
INTERPRO:
 IPR023058
INTERPRO:
 IPR027304
INTERPRO:
 IPR023034
INTERPRO:
 IPR015391
INTERPRO:
 IPR000297
MODBASE:
 P0ABZ6
PDB:
 2PV1
PDB:
 1M5Y
PDB:
 2PV3
PDB:
 2PV2
PFAM:
 PF13616
PFAM:
 PF09312
PFAM:
 PF00639
PRIDE:
 P0ABZ6
PRODB:
 PRO_000024015
PROSITE:
 PS01096
PROSITE:
 PS50198
REFSEQ:
 NP_414595
SMR:
 P0ABZ6
UNIPROT:
 P0ABZ6


Operon      
Name: lptD-surA-pdxA-rsmA-apaGH         
Operon arrangement:
Transcription unit        Promoter
apaGH
rsmA-apaGH
imp
imp
imp-surA-pdxA
pdxA-rsmA
pdxA-rsmA-apaGH
surA-pdxA-rsmA-apaGH


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_84 51998 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_86 52194 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_87 (cluster) 52478 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_88 52548 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_89 52587 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_90 53904 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_91 54275 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_92 54363 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_93 54605 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_94 54746 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_95 54754 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_96 (cluster) 54762 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_97 54765 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_98 54884 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_99 55120 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_100 55146 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_101 55785 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_102 (cluster) 55791 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_103 (cluster) 55800 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_104 55908 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_105 55916 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_106 55920 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_107 56036 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_108 (cluster) 56466 reverse nd [RS-EPT-CBR] [24]
  promoter TSS_109 56724 reverse nd [RS-EPT-CBR] [24]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Ades SE., Connolly LE., Alba BM., Gross CA., 1999, The Escherichia coli sigma(E)-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-sigma factor., Genes Dev 13(18):2449-61

 [2] Bothmann H., Pluckthun A., 2000, The periplasmic Escherichia coli peptidylprolyl cis,trans-isomerase FkpA. I. Increased functional expression of antibody fragments with and without cis-prolines., J Biol Chem 275(22):17100-5

 [3] Chai Q., Ferrell B., Zhong M., Zhang X., Ye C., Wei Y., 2014, Diverse sequences are functional at the C-terminus of the E. coli periplasmic chaperone SurA., Protein Eng Des Sel 27(4):111-6

 [4] Cook GM., Membrillo-Hernandez J., Poole RK., 1997, Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors., J Bacteriol 179(20):6525-30

 [5] Costello SM., Plummer AM., Fleming PJ., Fleming KG., 2016, Dynamic periplasmic chaperone reservoir facilitates biogenesis of outer membrane proteins., Proc Natl Acad Sci U S A 113(33):E4794-800

 [6] Dartigalongue C., Missiakas D., Raina S., 2001, Characterization of the Escherichia coli sigma E regulon., J Biol Chem 276(24):20866-75

 [7] Geitner AJ., Varga E., Wehmer M., Schmid FX., 2013, Generation of a highly active folding enzyme by combining a parvulin-type prolyl isomerase from SurA with an unrelated chaperone domain., J Mol Biol 425(22):4089-98

 [8] Jia M., Hu Y., Jin C., 2019, 1 H, 13 C and 15 N resonance assignments of the second peptidyl-prolyl isomerase domain of chaperone SurA from Escherichia coli., Biomol NMR Assign 13(1):183-186

 [9] Jia M., Wu B., Yang Z., Chen C., Zhao M., Hou X., Niu X., Jin C., Hu Y., 2020, Conformational Dynamics of the Periplasmic Chaperone SurA., Biochemistry 59(35):3235-3246

 [10] Jin F., 2020, The transmembrane supercomplex mediating the biogenesis of OMPs in Gram-negative bacteria assumes a circular conformational change upon activation., FEBS Open Bio 10(8):1698-1715

 [11] Ma HW., Buer J., Zeng AP., 2004, Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach., BMC Bioinformatics 5:199

 [12] Marx DC., Leblanc MJ., Plummer AM., Krueger S., Fleming KG., 2020, Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA., Protein Sci 29(10):2043-2053

 [13] Mogensen JE., Kleinschmidt JH., Schmidt MA., Otzen DE., 2005, Misfolding of a bacterial autotransporter., Protein Sci 14(11):2814-27

 [14] O'Reilly EK., Kreuzer KN., 2004, Isolation of SOS constitutive mutants of Escherichia coli., J Bacteriol 186(21):7149-60

 [15] Pease AJ., Roa BR., Luo W., Winkler ME., 2002, Positive growth rate-dependent regulation of the pdxA, ksgA, and pdxB genes of Escherichia coli K-12., J Bacteriol 184(5):1359-69

 [16] Rouviere PE., De Las Penas A., Mecsas J., Lu CZ., Rudd KE., Gross CA., 1995, rpoE, the gene encoding the second heat-shock sigma factor, sigma E, in Escherichia coli., EMBO J 14(5):1032-42

 [17] Rudd KE., Sofia HJ., Koonin EV., Plunkett G., Lazar S., Rouviere PE., 1995, A new family of peptidyl-prolyl isomerases., Trends Biochem Sci 20(1):12-4

 [18] Schiffrin B., Calabrese AN., Higgins AJ., Humes JR., Ashcroft AE., Kalli AC., Brockwell DJ., Radford SE., 2017, Effects of Periplasmic Chaperones and Membrane Thickness on BamA-Catalyzed Outer-Membrane Protein Folding., J Mol Biol 429(23):3776-3792

 [19] Vulic M., Kolter R., 2002, Alcohol-induced delay of viability loss in stationary-phase cultures of Escherichia coli., J Bacteriol 184(11):2898-905

 [20] Werner J., Augustus AM., Misra R., 2003, Assembly of TolC, a structurally unique and multifunctional outer membrane protein of Escherichia coli K-12., J Bacteriol 185(22):6540-7

 [21] Werner J., Misra R., 2005, YaeT (Omp85) affects the assembly of lipid-dependent and lipid-independent outer membrane proteins of Escherichia coli., Mol Microbiol 57(5):1450-9

 [22] Wu S., Ge X., Lv Z., Zhi Z., Chang Z., Zhao XS., 2011, Interaction between bacterial outer membrane proteins and periplasmic quality control factors: a kinetic partitioning mechanism., Biochem J 438(3):505-11

 [23] Zhong M., Ferrell B., Lu W., Chai Q., Wei Y., 2013, Insights into the Function and Structural Flexibility of the Periplasmic Molecular Chaperone SurA., J Bacteriol 195(5):1061-7

 [24] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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