Escherichia coli (strain K12) · seed P00722 · 1024 aa · family defined as ≥30% identity to that seed · compiled 07 October 2026
Open in CODSWALLOP UniProt P00722 RCSB by accession PDBe-KB AlphaFold DB InterPro CATH 2.60.120.260 CATH 2.60.40.10 CATH 3.20.20.80 CATH 2.70.98.10 SCOP 8037655 SCOP 8055209 SCOP 8037663 SCOP 8055462 SCOP 8037659 RCSB 3DYP PDBe
CATH and SCOP identifiers come from the RCSB's own structure annotations, which the Domains panel already reads, so these are looked up rather than guessed at.
Every figure here is counted over the whole family rather than quoted from one entry.
3DYP, the structure every other member of this family is superposed onto. Rendered by the RCSB and embedded here: the live app shows an interactive viewport, which a document that fetches nothing cannot.
How many of this family's constructs contain each residue of the seed. A trough is a stretch nobody has put in a construct, which is a construct-design answer rather than a disorder one.
49 distinct constructs across 116 entries. 102 polymer entities differ from the UniProt canonical sequence in some way, 36 carry a recognised expression tag and 0 carry a fusion partner.
"Differs from canonical" is not the same as "engineered". The canonical sequence is the full gene product, so a secreted protein whose structures all start after its signal peptide counts every one of them as different: lysozyme's most-used construct, residues 19–147 on 1,239 entities, is simply the mature protein. Read the construct column below for what was actually done, rather than this count.
| Entities | Length | Best (Å) | Best entry | What was made |
|---|---|---|---|---|
| 9 | 1023 | 1.50 | 1JZ7 | 1 internal deletion; M1S, T2H, I4L +2 more |
| 6 | 1010 | 1.50 | 6ZJS | E441Q |
| 6 | 1023 | 2.10 | 1JZ2 | residues 2-1024 |
| 5 | 1025 | 2.90 | 9WLN | matches the canonical sequence |
| 5 | 1031 | 2.20 | 9HPM | His6 |
| 4 | 1023 | 1.50 | 1JZ8 | 1 internal deletion; M1S, T2H, I4L +3 more |
| 4 | 1052 | 2.05 | 3VD9 | His6+T7; Enterokinase site; 1 internal deletion; M1D, T2P, T5D +2 more |
| 3 | 1010 | 2.12 | 6ZJW | D207A |
| 3 | 1010 | 2.23 | 6SED | matches the canonical sequence |
| 3 | 1023 | 2.10 | 3I3E | 1 internal deletion; M1S, T2H, I4L +3 more |
| 3 | 1024 | 2.20 | 6DRV | matches the canonical sequence |
| 3 | 1030 | 1.42 | 8RI8 | His6; F1008L |
| 3 | 1040 | 2.20 | 6TTE | His6; Thrombin site; 1 internal deletion; M1S, T2H, I4L +2 more |
| 3 | 1052 | 1.75 | 3T09 | His6+T7; Enterokinase site; 1 internal deletion; M1D, T2P, T5D +2 more |
| 3 | 1052 | 1.85 | 3T2O | His6+T7; Enterokinase site; 1 internal deletion; M1D, T2P, T5D +2 more |
| 3 | 1052 | 1.90 | 3MUZ | His6+T7; Enterokinase site; 1 internal deletion; M1D, T2P, T5D +2 more |
| 3 | 1052 | 1.90 | 3T0A | His6+T7; Enterokinase site; 1 internal deletion; M1D, T2P, T5D +2 more |
| 3 | 1052 | 2.05 | 3VDB | His6+T7; Enterokinase site; 1 internal deletion; M1D, T2P, T5D +2 more |
| 2 | 989 | 1.80 | 6ETZ | residues 22-1010 |
| 2 | 1012 | 1.70 | 6ZJQ | E517Q |
| 2 | 1021 | 1.80 | 6X1Q | residues 3-1023; E335V, E872V |
| 2 | 1021 | 1.90 | 9HKI | residues 3-1023 |
| 2 | 1021 | 2.80 | 1F4A | residues 4-1024 |
| 2 | 1022 | 2.20 | 5A1A | residues 3-1024 |
| 2 | 1023 | 1.60 | 1PX3 | 1 internal deletion; M1S, T2H, I4L +3 more |
Showing the 25 most-used of 49.
Columns where the wild-type residue still dominates but a real minority carries something else, which is a different question from "what varies across species".
| Oligomeric state | Chains | Entries | Share |
|---|---|---|---|
| tetrameric | 4 | 89 | 76.7% |
| dimeric | 2 | 19 | 16.4% |
| hexameric | 6 | 2 | 1.7% |
| octameric | 8 | 2 | 1.7% |
| trimeric | 3 | 1 | 0.9% |
| monomeric | 1 | 1 | 0.9% |
| dodecameric | 12 | 1 | 0.9% |
| 56-meric | 56 | 1 | 0.9% |
87 entries have the depositor's assembly corroborated by PISA, 24 carry the depositor's word alone and 5 were assigned by PISA where the depositor gave none. The middle figure is not a disagreement: PISA may have returned nothing or never run. 3 entries carry more than one assembly with different chain counts, so they have no single answer to quote: 3CZJ, 3DEC, 4TTG.
Every source's own domains on the seed axis, one row each. They are not merged: Pfam, CATH, SCOP and InterPro disagree about boundaries, and a merged track would state a consensus none of them gave.
| Domain | Source | Span (seed) | Chains |
|---|---|---|---|
| Galactose-binding domain-like | CATH 2.60.120.260 | 43–256 | 72 |
| Immunoglobulins | CATH 2.60.40.10 | 283–389 | 126 |
| Glycosidases | CATH 3.20.20.80 | 364–654 | 76 |
| 2.70.98.10 | CATH | 757–1024 | 70 |
| galactose-binding domain-like | SCOP2B 8037655 | 22–228 | 75 |
| beta-Galactosidase/glucuronidase domain-like | SCOP2B 8055209 | 229–342 | 75 |
| (Trans)glycosidases | SCOP2B 8037663 | 343–634 | 75 |
| beta-Galactosidase/glucuronidase domain-like | SCOP2B 8055462 | 635–739 | 75 |
| Galactose mutarotase-like | SCOP2B 8037659 | 740–1024 | 75 |
IPT12 entries
1498 entries
2DG3 entries
PTQ3 entries
1452 entries
2FG2 entries
GTZ2 entries
0MK2 entries
A1H052 entries
1471 entries
BGC1 entries
YGX1 entries
| Component | Class | Name | Entries | Best (Å) |
|---|---|---|---|---|
| NA | ion | Sodium Ion | 84 | 1.42 |
| MG | ion | Magnesium Ion | 84 | 1.42 |
| DMS | cryoprotectant | Dimethyl Sulfoxide | 52 | 1.50 |
| ACT | cryoprotectant | Acetate Ion | 14 | 1.50 |
| IPT | ligand | 1-Methylethyl 1-Thio-Beta-D-Galactopyranoside | 12 | 1.60 |
| GAL | cryoprotectant | Beta-D-Galactopyranose | 10 | 1.50 |
| MLI | buffer | Malonate Ion | 10 | 1.50 |
| 149 | ligand | D-Galactonolactone | 8 | 1.75 |
| BTB | buffer | 2-[Bis-(2-Hydroxy-Ethyl)-Amino]-2-Hydroxymethyl-Propane-1,3-Diol | 5 | 1.75 |
| GOL | cryoprotectant | Glycerol | 5 | 2.40 |
| FMT | buffer | Formic Acid | 5 | 1.50 |
| 2DG | ligand | 2-Deoxy-Alpha-D-Galactopyranose | 3 | 1.75 |
| CL | ion | Chloride Ion | 3 | 1.60 |
| K | ion | Potassium Ion | 3 | 1.60 |
| PTQ | ligand | 2-Phenylethyl 1-Thio-Beta-D-Galactopyranoside | 3 | 1.90 |
| 145 | ligand | 2-Nitrophenyl Beta-D-Galactopyranoside | 2 | 1.75 |
| 2FG | ligand | 2-Deoxy-2-Fluoro-Beta-D-Galactopyranose | 2 | 2.10 |
| GTZ | ligand | (5r, 6s, 7s, 8s)-5-Hydroxymethyl-6,7,8-Trihydroxy-Tetrazolo[1,5- | 2 | 2.10 |
| 0MK | ligand | Beta-L-Ribopyranose | 2 | 2.30 |
| A1H05 | ligand | (2s,3r,4s)-2-[Bis(Oxidanyl)methyl]pyrrolidine-3,4-Diol | 2 | 1.42 |
Parsed from the free text 87 depositors typed into
_exptl_crystal_grow.pdbx_details, out of 87
entries that recorded anything at all.
Median pH 6.5
(range 5.6 to 8.0).
110 entries carry a wwPDB validation report: 84 clean, 12 worth a check and 14 with something to explain. Median clashscore 5.05, median RSRZ outliers 2.26%, median R-free minus R-work 0.048. 110 have released structure factors.
| Organism | Entries | Best (Å) | Ligand-bound | Seed covered |
|---|---|---|---|---|
| Escherichia coli K-12 | 45 | 1.75 | 18 | 100% |
| Escherichia coli | 43 | 1.36 | 22 | 100% |
| Arthrobacter sp. 32cB | 17 | 1.50 | 3 | 94% |
| Thermotoga maritima MSB8 | 2 | 2.00 | 0 | 98% |
| Bacteroides thetaiotaomicron VPI-5482 | 2 | 2.10 | 0 | 98% |
| Kluyveromyces lactis | 2 | 2.75 | 0 | 94% |
| Arthrobacter sp. C2-2 | 1 | 1.90 | 0 | 96% |
| Phocaeicola vulgatus ATCC 8482 | 1 | 2.40 | 0 | 36% |
| Escherichia coli BL21 | 1 | 2.50 | 0 | 100% |
| Paenibacillus barengoltzii | 1 | 2.80 | 0 | 98% |
| Escherichia coli BL21(DE3) | 1 | 2.86 | 1 | 5% |
1024 residues, numbered every ten. Every identity figure in this document is measured against this sequence.
active or binding site modified residue or glycosylation disulphide cysteine transmembrane or signal the 15 most-substituted positions
Sites are UniProt's curated features where the seed is a UniProt accession; the substituted positions are measured from this family's own alignment rather than annotated, and only the fifteen most substituted are marked: every position carrying a minority substitution would be most of the protein, because the family holds orthologues. A residue can carry more than one and is drawn with the first that applies, in the order of the key above.
One record per paper, not per entry.
| Year | Citation |
|---|---|
| 2026 | Cryo-EM sample preparation with soft-landing and laser flash melting Nat Commun doi:10.1038/s41467-026-77723-6 |
| 2026 | Affinity-tag-based microfluidic protein isolation enables high-resolution Cryo-EM from minimal starting material Biorxiv doi:10.64898/2026.05.20.726462 |
| 2026 | The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis. Mol.Cell doi:10.1016/j.molcel.2025.12.022 |
| 2026 | Identification of Senescence-Associated beta-Galactosidase With Single-Molecule Resolution. Angew.Chem.Int.Ed.Engl. doi:10.1002/anie.5443283 |
| 2025 | Bacterial pathogen deploys the iminosugar glycosyrin to manipulate plant glycobiology. Science doi:10.1126/science.adp2433 |
| 2025 | MISO: microfluidic protein isolation enables single-particle cryo-EM structure determination from a single cell colony. Nat.Methods doi:10.1038/s41592-025-02894-x |
| 2025 | Nickel-NTA lipid-monolayer affinity grids allow for high-resolution structure determination by cryo-EM. J.Struct.Biol. doi:10.1016/j.jsb.2025.108253 |
| 2025 | Enhancing the synthesis efficiency of galacto-oligosaccharides of a beta-galactosidase from Paenibacillus barengoltzii by engineering the active and distal sites. Food Chem doi:10.1016/j.foodchem.2025.144208 |
| 2024 | Cryo-EM of soft-landed beta-galactosidase: Gas-phase and native structures are remarkably similar. Sci Adv doi:10.1126/sciadv.adl4628 |
| 2024 | SPOT-RASTR-A cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface. Pnas Nexus doi:10.1093/pnasnexus/pgae284 |
| 2023 | Time-resolved cryo-EM using a combination of droplet microfluidics with on-demand jetting. Nat.Methods doi:10.1038/s41592-023-01967-z |
| 2021 | Two-Dimensional Design Strategy to Construct Smart Fluorescent Probes for the Precise Tracking of Senescence. Angew.Chem.Int.Ed.Engl. doi:10.1002/anie.202101278 |
| 2020 | Mapping the Transglycosylation Relevant Sites of Cold-Adapted beta-d-Galactosidase fromArthrobactersp. 32cB. Int J Mol Sci doi:10.3390/ijms21155354 |
| 2020 | 1.8 angstrom resolution structure of beta-galactosidase with a 200 kV CRYO ARM electron microscope. Iucrj doi:10.1107/S2052252520006855 |
| 2020 | The cryo-EM Structure ofThermotoga maritimabeta-Galactosidase: Quaternary Structure Guides Protein Engineering. Acs Chem.Biol. doi:10.1021/acschembio.9b00752 |
| 2020 | Fragment-based drug discovery using cryo-EM. Drug Discov Today doi:10.1016/j.drudis.2019.12.006 |
| 2020 | First-generation species-selective chemical probes for fluorescence imaging of human senescence-associated beta-galactosidase. Chem Sci doi:10.1039/d0sc01234c |
| 2019 | Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-d-galactosidase fromArthrobactersp. 32cB. Int J Mol Sci doi:10.3390/ijms20174301 |
| 2019 | Structural features of cold-adapted dimeric GH2 beta-D-galactosidase from Arthrobacter sp. 32cB. Biochim Biophys Acta Proteins Proteom doi:10.1016/j.bbapap.2019.06.001 |
| 2018 | In Situ Random Microseeding and Streak Seeding Used for Growth of Crystals of Cold-Adapted Beta-D-Galactosidases: Crystal Structure of BetaDG from Arthrobacter sp. 32cB Crystals doi:10.3390/cryst8010013 |
| 2018 | Atomic Resolution Cryo-EM Structure of beta-Galactosidase. Structure doi:10.1016/j.str.2018.04.004 |
| 2018 | cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud. J. Struct. Biol. doi:10.1016/j.jsb.2018.05.014 |
| 2015 | Elucidating factors important for monovalent cation selectivity in enzymes: E. coli beta-galactosidase as a model. Phys Chem Chem Phys doi:10.1039/c4cp04952g |
| 2015 | 2.2 A Resolution Cryo-Em Structure of Beta-Galactosidase in Complex with a Cell-Permeant Inhibitor Science doi:10.1126/SCIENCE.AAB1576 |
| 2014 | Structure of beta-galactosidase at 3.2- angstrom resolution obtained by cryo-electron microscopy. Proc.Natl.Acad.Sci.USA doi:10.1073/pnas.1402809111 |
| 2014 | Molecular Mechanism of Antibody-Mediated Activation of Beta-Galactosidase. Structure doi:10.1016/J.STR.2014.01.011 |
| 2013 | Structural Explanation for Allolactose (lac operon inducer) Synthesis by lacZ beta-Galactosidase and the Evolutionary Relationship between Allolactose synthesis and the lac Repressor J.Biol.Chem. doi:10.1074/jbc.M113.455436 |
| 2012 | Ser-796 of Beta-Galactosidase (E. coli) Plays a Key Role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. doi:10.1016/j.abb.2011.11.017 |
| 2012 | Substitution for Asn460 cripples {beta}-galactosidase (Escherichia coli) by increasing substrate affinity and decreasing transition state stability. Arch.Biochem.Biophys. doi:10.1016/j.abb.2012.03.014 |
| 2012 | Structural basis of specificity in tetrameric Kluyveromyces lactis beta-galactosidase. J.Struct.Biol. doi:10.1016/j.jsb.2011.11.031 |
| 2010 | Importance of Arg-599 of b-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop Biochem.Cell Biol. |
| 2010 | Studies of Glu-416 variants of beta-galactosidase (E. coli) show that the active site Mg(2+) is not important for structure and indicate that the main role of Mg (2+) is to mediate optimization of active site chemistry Protein J. doi:10.1007/s10930-009-9216-x |
| 2010 | Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli). Biochem.Cell Biol. doi:10.1139/O10-009 |
| 2010 | Importance of Arg-599 of beta-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop Biochem.Cell Biol. doi:10.1139/O10-144 |
| 2009 | Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli). Protein Sci. doi:10.1002/pro.140 |
| 2009 | Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-beta-Galactosidase (E. coli) as Examples. Protein J. doi:10.1007/s10930-009-9168-1 |
| 2005 | Cold-active beta-Galactosidase from Arthrobacter sp. C2-2 Forms Compact 660kDa Hexamers: Crystal Structure at 1.9A Resolution J.Mol.Biol. doi:10.1016/j.jmb.2005.08.028 |
| 2003 | Structural Basis for the Altered Activity of Gly794 Variants of Escherichia coli Beta-Galactosidase Biochemistry doi:10.1021/bi035506j |
| 2001 | A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Biochemistry doi:10.1021/bi011727i |
| 2001 | Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J.Mol.Biol. doi:10.1006/jmbi.2001.4891 |