Table 1.
General information on USP crystal structures deposited in the Protein Data Bank (PDB)
| Name | PDB code | Organisms | Annot. | ATP-rel. | ATP-binding motif | Motif | ATP | Ion | SG center | Ref. |
|---|---|---|---|---|---|---|---|---|---|---|
| NE1028 | 2PFS/3TNJ | N. europea | USP | D12, V40 | G114-SH-G117-(8X)-G126ST | Typical | No/AMP | No | MCSG | –* |
| AF0836 | 3DLO/3QTB | A. fulgidus | USP | D11, S40 | G103-IR-K106 -(9X)-G116SV | Typical | No/dAMP | Cl | MCSG | –3 |
| AF1760 | 3LOQ | A. fulgidus | USP | D154,V182 | G234-SR-G237-(9X)-G247ST | Typical | AMP | Cl | MCSG | n/a |
| Lp1163 | 3S3T | L. plantarum | USP | D13, V41 | G115-AT-G118-(9X)-G128ST | Typical | ATP | Ca | MCSG | n/a |
| Lp3663 | 3FG9 | L. plantarum | UspA | D20, V50 | G123-AD-T126-(11X)-G138PR | Degen. | No | Mg | MCSG | n/a |
| WS0661 | 3IDF | W. succinogenes | USP | D9, V38 | G108-SS-E111-(8X)-A120SH | Degen. | No | No | MCSG | n/a |
| Rv2623 | 3CIS | M. tuberculosis | UspE | D167,A195 | G262-SR-G265-(9X)-G275SV | Typical | ATP | Mg | MCSG | n/a |
| Rv1636 | 1TQ8 | M. tuberculosis | D25, A52 | G126-NV-G129-(9X)-G139SV | Typical | No | No | NYSGXRC | n/a | |
| Rv2623 | 2JAX | M. tuberculosis | UspE | D167,A195 | G262-SR-G265-(9X)-G275SV | Typical | ATP | No | n/a | n/a |
| KPN01444 | 3FH0 | Klebsiella pneumoniae | USP | D7, V37 | A111-SH-R114-(8X)-G123SN | Degen. | ADP | No | MCSG | n/a |
| KPN01444 | 3FDX | K. pneumoniae | UspF | D7, V37 | A111-SH-R114-(8X)-G123SN | Degen. | ATP | Mg | MCSG | n/a |
| AT3G01520 | 2GM3 | A. thaliana | USP | N13, V53 | G131-SR-G134-(9X)-G275SV | Typical | AMP | No | CESG | n/a |
| Aq178 | 1Q77 | A. aeolicus | UspA | D9, V37 | A113-CY-P130 | Degen. | No | No | MCSG | n/a |
| PMI1202 | 3OLQ | P. mirabilis | UspE | N161,A198 | G270-IL-G273-(10X)-N284TA | Degen. | No | No | MCSG | n/a |
| PA1789 | 3MT0† | Pseudomonas aeruginosa | UspE | D139,A174 | G241-TV-A244-(9X)-G254NT | Degen. | No | Cl | MCSG | n/a |
| 1WJG | T. thermophilusHB8 | –‡ | D10, A38 | G106-TR-G109-(9X)-G119SQ | Typical | No | No | RSGI | n/a | |
| TTHA0895 | 2Z3V | T. thermophilusHB8 | USP | D10, A38 | G106-TR-G109-(9X)-G119SQ | Typical | No | No | RSGI | n/a |
| TTHA0895 | 2Z08/9 | T. thermophilusHB8 | USP | D10, A38 | G106-TR-G109-(9X)-G119SQ | Typical | ATP/ACT | Mg | RSGI | n/a |
| TTH0350 | 3AB7/8 | T. thermophilus HB8 | USP | D8, V36 | G121-RS-D124-(5X)-G130ST | Degen. | ATP | Mg | n/a | (1) |
| HI0815 | 1JMV | H. influenzae | UspA | D10, A38 | G109-HH-Q112-(6X)-M119SV | Degen. | No | No | n/a | (2) |
| HELO1754 | 3HGM | H. elongata | TeaD | D10, A38 | G117-AE-G120-(9X)-G130SV | Degen. | ATP | Mn | n/a | (3) |
| MJ0577 | 1MJH | M. jannaschii | –‡ | D13, V41 | G127-SH-G130-(9X)-G140SV | Typical | ATP | Mn | BSGC | (4) |
MCSG, Midwest Center for Structural Genomics; RSGI, RIKEN Structural Genomics/Proteomics Initiative; CESG, Center for Eukaryotic Structural Genomics; BSGC, Berkley Structural Genomics Center; NYSGXRC, New York SGX Research Consortium.
X denotes structures not solved by structural genomics centers.
This work, X denotes any residue and the digit in front of it the number of X residues. AMP, ADP, and ACT are the following derivatives of ATP: ACT, phosphomethylphosphonic acid adenylate ester (C11H18N5O13P3); AMP, adenosine monophosphate (C10H14N5O7P); ADP, adenosine-5′-diphosphate (C10H15N5O10P2). (i) publication by Iino et al. (2011), (ii) work by Sousa and McKay (2001), (iii) publication by Schweikhard et al. (2010), (iv) work by Zarembinski et al. (1998).
Special case of USP.
ATP-binding protein.