Proteins with multiple sub-cellular topologies in E.coli K-12 (MG1655)

UniProt Name:
RNA polymerase sigma factor RpoD (Sigma-70)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Trigger factor-sensitive aggregation.
References:
PMID: 19737520 PMID: 23138451 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
306 ppm

Class:
All alpha proteins
SCOP: 46456
Fold:
DNA/RNA-binding 3-helical bundle
SCOP: 46688
Sigma2 domain of RNA polymerase sigma factors
SCOP: 88945
Super Family:
Sigma3 and sigma4 domains of RNA polymerase sigma factors
SCOP: 88659
Sigma2 domain of RNA polymerase sigma factors
SCOP: 88946

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UniProt Name:
DNA polymerase I (POL I) (EC 2.7.7.7)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
-
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
4

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
40
PaxDb:
188 ppm

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
SAM domain-like
SCOP: 47768
Ribonuclease H-like motif
SCOP: 53066
DNA/RNA polymerases
SCOP: 56671
PIN domain-like
SCOP: 88722
Super Family:
5' to 3' exonuclease, C-terminal subdomain
SCOP: 47807
Ribonuclease H-like
SCOP: 53098
DNA/RNA polymerases
SCOP: 56672
PIN domain-like
SCOP: 88723

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UniProt Name:
Alanine--tRNA ligase (EC 6.1.1.7) (Alanyl-tRNA synthetase) (AlaRS)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Trigger factor-sensitive aggregation.
References:
PMID: 19737520 PMID: 23138451 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
9

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
86
PaxDb:
412 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Reductase/isomerase/elongation factor common domain
SCOP: 50412
RRF/tRNA synthetase additional domain-like
SCOP: 55185
Class II aaRS and biotin synthetases
SCOP: 55680
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
SCOP: 101352
Super Family:
Translation proteins
SCOP: 50447
ThrRS/AlaRS common domain
SCOP: 55186
Class II aaRS and biotin synthetases
SCOP: 55681
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
SCOP: 101353

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UniProt Name:
Chromosomal replication initiator protein DnaA
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
C-terminal amphiphilic helix (355-370). Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 10660626 PMID: 23138451 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
7

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
27
PaxDb:
31.3 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
P-loop containing nucleoside triphosphate hydrolases SCOP: 52539
Super Family:
TrpR-like
SCOP: 48295
P-loop containing nucleoside triphosphate hydrolases
SCOP: 52540

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UniProt Name:
GTPase Era (ERA) (GTP-binding protein Era)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm & ribosomal
Notes:
Assembly cofactor of ribosome; associate with the 30S subunit and 16S rRNA. YeaA has been viewed through fluorescence microscopy and located evenly throughout cytoplasm. Small scale study of labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes. PMID: 17272300
References:
PMID: 17272300 PMID: 21529161 PMID: 8282709
Pseudogene/Mobile Element:
-

mRNA molec/cell:
7

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
0
PaxDb:
35.3 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Alpha-lytic protease prodomain-like SCOP: 54805
Super Family:
P-loop containing nucleoside triphosphate hydrolases
SCOP: 52540
Prokaryotic type KH domain (KH-domain type II)
SCOP: 54814

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UniProt Name:
Bifunctional ligase/repressor BirA (Biotin operon repressor) (Biotin--[acetyl-CoA-carboxylase] ligase) (EC 6.3.4.15) (Biotin--protein ligase) (Biotin-[acetyl-CoA carboxylase] synthetase)
Localization:
Integral Inner Membrane, Nucleoid
Notes:
-
References:
PMID: 23138451 PMID: 23387333
Pseudogene/Mobile Element:
-

mRNA molec/cell:
2

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
9
PaxDb:
15 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Class II aaRS and biotin synthetases SCOP: 55680
Super Family:
Winged helix DNA-binding domain
SCOP: 46785
C-terminal domain of transcriptional repressors
SCOP: 50037
Class II aaRS and biotin synthetases
SCOP: 55681

Orientation on the IM:
(N-terminus/C-terminus)

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UniProt Name:
HTH-type transcriptional regulator MalT (ATP-dependent transcriptional activator MalT)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Cytoplasmic transciption factor that binds maltotriose and ATP and shuttles between the chromosome and membranes as a peripheral protein on the MalK peripheral ATPase of the maltose transporter. Trigger factor-sensitive aggregation. LuxR-type HTH domain signature and profile. The luxR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators (PROSITE: PDOC0054).
References:
PMID: 15063852 PMID: 19737520 PMID: 23138451
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 19767571 PMID: 15115803 PMID: 17446557 PMID: 20923772
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
51.3 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
P-loop containing nucleoside triphosphate hydrolases SCOP: 52539
Super Family:
C-terminal effector domain of the bipartite response regulators
SCOP: 46894
TPR-like
SCOP: 48452
P-loop containing nucleoside triphosphate hydrolases
SCOP: 52540

Go to Complexes

UniProt Name:
Bifunctional protein PutA [Includes: Proline dehydrogenase (EC 1.5.5.2) (Proline oxidase); Delta-1-pyrroline-5-carboxylate dehydrogenase (P5C dehydrogenase) (EC 1.2.1.88) (L-glutamate gamma-semialdehyde dehydrogenase)]
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
The proline dehydrogenase PutA protein from S. typhimurium was shown to act as a membrane-associated enzyme or as a transcriptional repressor PMID: 8483946. Catabolism of proline requires PutA to associate with the membrane because reoxidation of the FAD cofactor in PutA needs the presence of an electron acceptor. Repression of the put operon requires PutA to bind to the put control-region DNA in the cytoplasm. Transcription factor PMID: 23138451. Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 23138451 PMID: 23230279 PMID: 8483946
Pseudogene/Mobile Element:
-

mRNA molec/cell:
0

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein molec/cell:
12
PaxDb:
42.4 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
N-terminal domain of bifunctional PutA protein SCOP: 81934
Super Family:
Ribbon-helix-helix
SCOP: 47598
FAD-linked oxidoreductase
SCOP: 51730
ALDH-like
SCOP: 53720
N-terminal domain of bifunctional PutA protein
SCOP: 81935

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UniProt Name:
GTPase Der (Double era-like domain protein) (GTP-binding protein EngA)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm & ribosomal
Notes:
Essential protein, proposed to be engaged in a functional cyclic interaction between ribosomes and the membrane in Escherichia coli through interaction with the 50S subunit. Assembly cofactor of ribosome; associates with the 50S subunit and YihI. YeaA has been viewed through fluorescence microscopy and located evenly throughout cytoplasm. Small scale study of labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes. PMID: 17272300 Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 11387344 PMID: 16930151 PMID: 17272300 PMID: 20172997 PMID: 21354313 PMID: 21529161 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
23
PaxDb:
172 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
P-loop containing nucleoside triphosphate hydrolases SCOP: 52539
Super Family:
P-loop containing nucleoside triphosphate hydrolases
SCOP: 52540

Go to Complexes

UniProt Name:
Enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (2-phosphoglycerate dehydratase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Peripheral outer membrane protein facing the extra-cellular space
Notes:
When modified at Lys342 possibly secreted by an unknown mechanism, no evidence of signal peptide) Homodimer, stabilized by Mg2+; Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. Essential for the degradation of carbohydrates via glycolysis. Also a component of the RNA degradosome. The covalent binding to the substrate at Lys-342 causes inactivation of the enzyme, and possibly serves as a signal for the export of the protein. Interacts with the C-terminal region of the endoribonuclease RNase EIn the RNA degradosome. Fractions of enolase are present in both the cytoplasm and on the cell surface. As part of the bacterial cytoskeleton in the cytoplasm,Is organized as extended coiled structures that wind around the cell, from one cell pole to the other. When covalently bound to the substrate at Lys-342, the inactive enolase is secreted, and remains attached to the bacterial cell surface. PMID: 8610017 PMID: 9600841 PMID: 9740056 PMID: 9732527 PMID: 12035760 Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 12035760 PMID: 15003462 PMID: 17242352 PMID: 18337249 PMID: 23230279 PMID: 8610017 PMID: 9600841 PMID: 9732527 PMID: 9740056
Pseudogene/Mobile Element:
-

mRNA molec/cell:
21

Proteomics:
PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 20521846 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18425732
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein molec/cell:
567
PaxDb:
3361 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Enolase N-terminal domain-like SCOP: 54825
Super Family:
Enolase C-terminal domain-like
SCOP: 51604
Enolase N-terminal domain-like
SCOP: 54826

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UniProt Name:
DNA-binding protein Fis (Factor-for-inversion stimulation protein) (Hin recombinational enhancer-binding protein)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Nucleoid-associated protein (NAP).
References:
PMID: 21541338 PMID: 23138451 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 20222674 PMID: 19767571 PMID: 20803007 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
224 ppm

Class:
All alpha proteins
SCOP: 46456
Fold:
DNA/RNA-binding 3-helical bundle SCOP: 46688
Super Family:
Homeodomain-like
SCOP: 46689

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UniProt Name:
RNA-binding protein Hfq (HF-1) (Host factor-I protein) (HF-I)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Nucleoid
Notes:
The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain. Is a bacterial protein involved in several aspects of nucleic acid transactions. Nucleoid-associated protein (NAP) that binds sequence-nonspecific DNA. Part of membrane-associating assemblies that coil around the periphery of the cell when visualized by immunofluorescence microscopy. These assemblies co-localize with the RNA degradosome and participate in the RNA degradation process. PMID: 24438330
References:
PMID: 20011543 PMID: 21541338 PMID: 24438330
Pseudogene/Mobile Element:
-

mRNA molec/cell:
46

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 19767571 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
1513
PaxDb:
1334 ppm

Class:
All beta proteins
SCOP: 48724
Fold:
Sm-like fold SCOP: 50181
Super Family:
Sm-like ribonucleoproteins
SCOP: 50182

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UniProt Name:
Integration host factor subunit alpha (IHF-alpha)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Translation. Experimentally verified gene-product. Methionine start codon is cleaved. Identified in nucleoids collected by sucrose gradient centrifugation and analyzed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS)PMID: 21541338. Bacterial histone-like DNA-binding proteins signature
References:
PMID: 21541338 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
2070 ppm

Class:
All alpha proteins
SCOP: 46456
Fold:
IHF-like DNA-binding proteins SCOP: 47728
Super Family:
IHF-like DNA-binding proteins
SCOP: 47729

Go to Complexes

UniProt Name:
Integration host factor subunit beta (IHF-beta)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Translation, nucleoid-associated protein (NAP). Bacterial histone-like DNA-binding proteins signature
References:
PMID: 21541338 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
1227 ppm

Class:
All alpha proteins
SCOP: 46456
Fold:
IHF-like DNA-binding proteins SCOP: 47728
Super Family:
IHF-like DNA-binding proteins
SCOP: 47729

Go to Complexes

UniProt Name:
Translation initiation factor IF-2
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm & ribosomal
Notes:
Translation. Trigger factor-sensitive aggregation.
References:
PMID: 19737520 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
380 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
P-loop containing nucleoside triphosphate hydrolases SCOP: 52539
Super Family:
Putative DNA-binding domain
SCOP: 46955
Translation proteins
SCOP: 50447
Initiation factor IF2/eIF5b, domain 3
SCOP: 52156
P-loop containing nucleoside triphosphate hydrolases
SCOP: 52540

Go to Complexes

UniProt Name:
Translation initiation factor IF-3 [Cleaved into: Translation initiation factor IF-3, N-terminally processed; Translation initiation factor IF-3S]
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm & ribosomal
Notes:
Translation. Trigger factor-sensitive aggregation. Evidence that the inter-domain region is disordered in solution.
References:
PMID: 19737520 PMID: 23230279 PMID: 9054966
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
801 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
IF3-like SCOP: 55199
Super Family:
Translation initiation factor IF3, N-terminal domain
SCOP: 54364
Translation initiation factor IF3, C-terminal domain
SCOP: 55200

Go to Complexes

UniProt Name:
RNA pyrophosphohydrolase (EC 3.6.1.-) ((Di)nucleoside polyphosphate hydrolase) (Ap5A pyrophosphatase)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Part of membrane-associating assemblies that coil around the periphery of the cell when visualized by immunofluorescence microscopy. These assemblies co-localize with the RNA degradosome and participate in the RNA degradation process. PMID: 24438330
References:
PMID: 24438330
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 19348461 PMID: 20222674
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
35
PaxDb:
30 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Nudix SCOP: 55810
Super Family:
Nudix
SCOP: 55811

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UniProt Name:
DNA replication and repair protein RecF
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Experimentally detected by proteomics analysis of E.coli membrane fraction (Bernsel et al 2009). No transmembrane helix is predicted. Weak hydrophobic and non cytoplasmic regions predicted by Phobius. Potential peripherally associated protein facing the cytoplasm or integral inner membrane protein. The prokaryotic protein recF is a single-stranded DNA-binding protein which also probably binds ATP. RecF is involved in DNA metabolism; it is required for recombinational DNA repair and for induction of the SOS response. PMID: 1542576
References:
PMID: 1542576 PMID: 19766000
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 20932056
Proteomics / Inner Membrane fraction:
PMID: 17309111

Protein molec/cell:
-
PaxDb:
0 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
P-loop containing nucleoside triphosphate hydrolases SCOP: 52539
Super Family:
P-loop containing nucleoside triphosphate hydrolases
SCOP: 52540

Go to Complexes

UniProt Name:
Ribosome maturation factor RimM (21K)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm & ribosomal
Notes:
Assembly cofactor of ribosome; associate with the 30S subunit. PMID: 11514519 Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 11514519 PMID: 21529161 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 12488465 PMID: 20222674 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
136 ppm

Class:
All beta proteins
SCOP: 48724
Fold:
Reductase/isomerase/elongation factor common domain SCOP: 50412
Super Family:
PRC-barrel domain
SCOP: 50346
Translation proteins
SCOP: 50447

Go to Complexes

UniProt Name:
Ribonuclease 3 (EC 3.1.26.3) (Ribonuclease III) (RNase III)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm
Notes:
Copurifies with trigger factor in pull down assays. Part of membrane-associating assemblies that coil around the periphery of the cell when visualized by immunofluorescence microscopy. These assemblies co-localize with the RNA degradosome and participate in the RNA degradation process. PMID: 24438330
References:
PMID: 19737520 PMID: 24438330 PMID: 4865702
Pseudogene/Mobile Element:
-

mRNA molec/cell:
12

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056 PMID: 20923772
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
69
PaxDb:
141 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
RNase III domain-like SCOP: 69064
Super Family:
dsRNA-binding domain-like
SCOP: 54768
RNase III domain-like
SCOP: 69065

Go to Complexes