E. coli K-12 / MG1655/ ATCC 47076 proteome

UniProt Name:
Transcriptional regulatory protein RcsB (Capsular synthesis regulator component B)
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm (Experimental) Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm (Potential)
Notes:
Regulator protein RcsB is a member of the two-component regulatory system RcsC/RcsB. It is involved in the activation of colanic acid capsule synthesis (cps) and cell division (ftsZ) genes. It is believed that the RcsB protein is activated through phosphorylation, probably by the sensor protein RcsC. RcsB protein for Regulator capsule synthesis B, is a response regulator that belongs to the multicomponent RcsF/RcsC/RcsD/RcsA-RcsB phosphorelay system. 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: 2404948
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 20923772
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
368
PaxDb:
662 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Flavodoxin-like SCOP: 52171
Super Family:
C-terminal effector domain of the bipartite response regulators
SCOP: 46894
CheY-like
SCOP: 52172

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UniProt Name:
Trifunctional NAD biosynthesis/regulator protein NadR [Includes: Transcriptional regulator NadR; Nicotinamide mononucleotide adenylyltransferase (NMN adenylyltransferase) (NMN-AT) (NMNAT) (EC 2.7.7.1) (Nicotinamide ribonucleotide adenylyltransferase) (Nicotinamide-nucleotide adenylyltransferase); Ri
Localization:
Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm (Experimental) Cytoplasmic, Nucleoid, Peripheral inner membrane protein facing the cytoplasm (Probable)
Notes:
May loosely associate with the membrane through its interaction with the membrane-bound pnuC (Nicotinamide riboside transporter). In combination with corepressor (NAD?), the cytoplasmic form of nadR would be capable of acting as a transcriptional repressor. Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 10464228 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:
25.7 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
P-loop containing nucleoside triphosphate hydrolases SCOP: 52539
Super Family:
lambda repressor-like DNA-binding domains
SCOP: 47413
Nucleotidylyl transferase
SCOP: 52374
P-loop containing nucleoside triphosphate hydrolases
SCOP: 52540

Go to Complexes

UniProt Name:
D-alanyl-D-alanine-carboxypeptidase/endopeptidase AmpH (EC 3.4.-.-) (DD-alanine-endopeptidase) (DD-carboxypeptidase) (Penicillin-binding protein AmpH)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Probable)
Notes:
Potential substrate of periplasmic peptidyl prolyl cis???trans isomerase SurA. Sequence contains known binding motif of SurA [RYEF]X[RYEF][P]. The N-terminal export signal of AmpH is processed, but the protein remains membrane associated. Disulfide bond-containing protein PMID: 25664544
References:
PMID: 22001512
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 19767571
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
2.39 ppm

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
beta-lactamase/transpeptidase-like
SCOP: 56600
Super Family:
beta-lactamase/transpeptidase-like
SCOP: 56601

Go to Complexes

UniProt Name:
L-Ala-D/L-Glu epimerase (AE epimerase) (AEE) (EC 5.1.1.20)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Potential)
Notes:
No transmembrane helix is predicted. Weak hydrophobic and non cytoplasmic regions predicted by Phobius. No transmembrane helix is predicted. Weak hydrophobic and non cytoplasmic regions predicted by Phobius.
References:
-
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 20222674 PMID: 15115803
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
24.9 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

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 (Experimental) Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Peripheral outer membrane protein facing the extra-cellular space (Potential) Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm, Peripheral outer membrane protein facing the extra-cellular space (Probable)
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

Go to Complexes

UniProt Name:
Chaperone protein DnaK (HSP70) (Heat shock 70 kDa protein) (Heat shock protein 70)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental) Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Probable)
Notes:
DnaK associates with the inner membrane. The ability to isolate DnaK with a membrane fraction prepared under gentle lysis conditions supports a peripheral association between DnaK and the cytoplasmic membrane. PMID: 7961473 Overexpression of three different membrane proteins (YidC, YedZ, and LepI) fused to green fluorescent protein (GFP) led to an increased association (2.3???4.8-fold) of DnaK with the membrane. PMID: 17446557 PMID: 1396676 PMID: 7783627 Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279 Interacts with DmsD is a redox enzyme maturation protein (REMP). PMID: 20153451
References:
PMID: 1396676 PMID: 16079137 PMID: 17446557 PMID: 20153451 PMID: 23230279 PMID: 7783627
Pseudogene/Mobile Element:
-

mRNA molec/cell:
15

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 16079137 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603 PMID: 20923772 PMID: 18425732
Proteomics / Inner Membrane fraction:
PMID: 16079137 PMID: 17446557 PMID: 17309111

Protein molec/cell:
2435
PaxDb:
4132 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Heat shock protein 70kD (HSP70), peptide-binding domain SCOP: 100919
Super Family:
Actin-like ATPase domain
SCOP: 53067
Heat shock protein 70kD (HSP70), peptide-binding domain
SCOP: 100920
Heat shock protein 70kD (HSP70), C-terminal subdomain
SCOP: 100934

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UniProt Name:
Lipoprotein-releasing system ATP-binding protein LolD (EC 3.6.3.-)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
-
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
56
PaxDb:
122 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:
1,2-phenylacetyl-CoA epoxidase, subunit C (1,2-phenylacetyl-CoA epoxidase, structural subunit beta) (1,2-phenylacetyl-CoA monooxygenase, subunit C)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Probable)
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.
References:
PMID: 19766000
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
2.37 ppm

Class:
All alpha proteins
SCOP: 46456
Fold:
Ferritin-like SCOP: 47239
Super Family:
Ferritin-like
SCOP: 47240

Go to Complexes

UniProt Name:
1-deoxy-D-xylulose-5-phosphate synthase (EC 2.2.1.7) (1-deoxyxylulose-5-phosphate synthase) (DXP synthase) (DXPS)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
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: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
59
PaxDb:
82.2 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
TK C-terminal domain-like SCOP: 52921
Super Family:
Thiamin diphosphate-binding fold (THDP-binding)
SCOP: 52518
TK C-terminal domain-like
SCOP: 52922

Go to Complexes

UniProt Name:
10 kDa chaperonin (GroES protein) (Protein Cpn10)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
-
References:
PMID: 20153451 PMID: 22380631 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603 PMID: 20923772
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
2150
PaxDb:
3789 ppm

Class:
All beta proteins
SCOP: 48724
Fold:
GroES-like SCOP: 50128
Super Family:
GroES-like
SCOP: 50129

Go to Complexes

UniProt Name:
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) (Tetrahydrodipicolinate N-succinyltransferase) (THDP succinyltransferase) (THP succinyltransferase) (Tetrahydropicolinate succinylase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
-
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 15115803 PMID: 20932056 PMID: 18796603
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
-
PaxDb:
844 ppm

Class:
All beta proteins
SCOP: 48724
Fold:
Single-stranded left-handed beta-helix SCOP: 51160
Super Family:
Trimeric LpxA-like enzymes
SCOP: 51161

Go to Complexes

UniProt Name:
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (BPG-dependent PGAM) (PGAM) (Phosphoglyceromutase) (dPGM) (EC 5.4.2.11)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
-
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 19348461 PMID: 20222674 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 18796603 PMID: 20923772
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
760
PaxDb:
2951 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Phosphoglycerate mutase-like SCOP: 53253
Super Family:
Phosphoglycerate mutase-like
SCOP: 53254

Go to Complexes

UniProt Name:
2-amino-3-ketobutyrate coenzyme A ligase (AKB ligase) (EC 2.3.1.29) (Glycine acetyltransferase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
Trigger factor-sensitive aggregation.
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 16606699 PMID: 12624733 PMID: 12488465 PMID: 17137328 PMID: 19348461 PMID: 20222674 PMID: 19767571 PMID: 15115803 PMID: 20932056
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
23
PaxDb:
146 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
PLP-dependent transferase-like
SCOP: 53382
Super Family:
PLP-dependent transferases
SCOP: 53383

Go to Complexes

UniProt Name:
2-iminobutanoate/2-iminopropanoate deaminase (EC 3.5.99.10) (Enamine/imine deaminase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
Experimentally verified gene-product. Methionine start codon is cleaved. Detected in acossiation with the inner membrane (sequential biochemical fractionations coupled with high resolution mass spectrometry). PMID: 23230279
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 19348461 PMID: 20222674 PMID: 16858726 PMID: 19767571 PMID: 20803007 PMID: 15115803 PMID: 18796603 PMID: 18425732
Proteomics / Inner Membrane fraction:
-

Protein molec/cell:
1164
PaxDb:
2464 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Bacillus chorismate mutase-like
SCOP: 55297
Super Family:
YjgF-like
SCOP: 55298

Go to Complexes

UniProt Name:
2-octaprenyl-6-methoxyphenol hydroxylase (EC 1.14.13.-)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Probable)
Notes:
The biosynthesis of UQ is studied in great detail in bacteria and yeast but only to a limited extent in animal tissues. The UQ biosynthetic enzymes may constitute a complex that is tightly bound to the membrane.
References:
PMID: 11583838
Pseudogene/Mobile Element:
-

mRNA molec/cell:
1

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

Protein molec/cell:
12
PaxDb:
10.9 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
FAD/NAD(P)-binding domain SCOP: 51904
Super Family:
FAD/NAD(P)-binding domain
SCOP: 51905

Go to Complexes

UniProt Name:
2-oxoglutarate dehydrogenase E1 component (EC 1.2.4.2) (Alpha-ketoglutarate dehydrogenase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
Trigger factor-sensitive aggregation.
References:
PMID: 15919657 PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

Proteomics:
PMID: 12624733 PMID: 12488465 PMID: 19348461 PMID: 20222674 PMID: 19003857 PMID: 16967446 PMID: 16858726 PMID: 19767571 PMID: 15919657 PMID: 15115803 PMID: 20932056 PMID: 17446557 PMID: 20923772
Proteomics / Inner Membrane fraction:
PMID: 15919657

Protein molec/cell:
158
PaxDb:
485 ppm

Class:
Alpha and beta proteins (a/b)
SCOP: 51349
Fold:
Thiamin diphosphate-binding fold (THDP-binding)
SCOP: 52517
Super Family:
Thiamin diphosphate-binding fold (THDP-binding)
SCOP: 52518

Go to Complexes

UniProt Name:
2-succinylbenzoate--CoA ligase (EC 6.2.1.26) (o-succinylbenzoyl-CoA synthetase) (OSB-CoA synthetase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (By similarity)
Notes:
Homologous to FadD13 protein of Mycobacterium that is peripheral.
References:
PMID: 22560731
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
0.787 ppm

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
Acetyl-CoA synthetase-like SCOP: 56800
Super Family:
Acetyl-CoA synthetase-like
SCOP: 56801

Go to Complexes

UniProt Name:
23S rRNA pseudouridine(2604) synthase (EC 5.4.99.21) (Ribosomal large subunit pseudouridine synthase F) (rRNA pseudouridylate synthase F) (rRNA-uridine isomerase F)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Experimental)
Notes:
-
References:
PMID: 23230279
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
9.71 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
Pseudouridine synthase SCOP: 100877
Super Family:
Pseudouridine synthase
SCOP: 55120
Alpha-L RNA-binding motif
SCOP: 55174

Go to Complexes

UniProt Name:
3'(2'),5'-bisphosphate nucleotidase CysQ (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydrolase) (3'-phosphoadenosine 5'-phosphate phosphatase) (PAP phosphatase) (DPNPase)
Localization:
Cytoplasmic, Peripheral inner membrane protein facing the cytoplasm (Probable)
Notes:
Identified in the inner membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry. PMID: 15911532 PMID: 15911532
References:
PMID: 15911532
Pseudogene/Mobile Element:
-

mRNA molec/cell:
-

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

Protein molec/cell:
-
PaxDb:
286 ppm

Class:
Multi-domain proteins (alpha and beta)
SCOP: 56572
Fold:
Carbohydrate phosphatase
SCOP: 56654
Super Family:
Carbohydrate phosphatase
SCOP: 56655

Go to Complexes

UniProt Name:
3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase) (EC 4.1.99.12)
Localization:
-
Notes:
-
References:
-
Pseudogene/Mobile Element:
-

mRNA molec/cell:
6

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

Protein molec/cell:
178
PaxDb:
162 ppm

Class:
Alpha and beta proteins (a+b)
SCOP: 53931
Fold:
YrdC/RibB SCOP: 55820
Super Family:
YrdC/RibB
SCOP: 55821

Go to Complexes