Table 2.
Summary of new enolase and amidohydrolase X-ray crystal structures and automated template-based modeling results, including subgroup and family assignments
| PDB code | Database accession number (Genpept GI IDs) | No of sequences in Psi-blast alignment | No of sequences with acceptable models and/or fold assignments | No of models >50% seq. ID (min 50% template coverage) | No of models 30–50% seq. ID (min 50% template coverage) | No of models <30% seq. ID (min 50% template coverage) | Subgroup assignment | Family assignment |
|---|---|---|---|---|---|---|---|---|
| Enolase super family | ||||||||
| 2GL5 | 16420812 | 2,863 | 2,777 | 0 | 98 | 2,462 | Mandelate racemase-like | Galactonate dehydratase |
| 2GDQ | 2633433 | 2,234 | 2,129 | 1 | 0 | 2,036 | Mandelate racemase-like | None |
| 2GSH | 16420830 | 2,588 | 2,286 | 16 | 9 | 2,110 | Mandelate racemase-like | l-Fuconate dehydratase |
| 2HNE | 21115341 | 2,746 | 2,712 | 83 | 20 | 2,527 | Mandelate racemase-like | None |
| 2HZG | 77386310 | 2,667 | 2,341 | 1 | 1 | 2,248 | Mandelate racemase-like | None |
| 2I5Q | 15832389 | 2,566 | 2,340 | 21 | 13 | 2,206 | Mandelate racemase-like | None |
| 2NQL | 17743914 | 2,849 | 2,470 | 2 | 1 | 2,356 | Mandelate racemase-like | None |
| 2O56 | 16767118 | 3,016 | 2,968 | 15 | 127 | 2,735 | Mandelate racemase-like | None |
| 2OQH | 21225834 | 2,690 | 2,668 | 2 | 32 | 2,630 | Glucarate dehydratease-like | None |
| 2OQY | 23100298 | 2,700 | 2,631 | 1 | 0 | 3,004 | Muconate cycloisomerase-like | None |
| 2OVL | 21221904 | 2,670 | 2,656 | 1 | 97 | 2,534 | Mandelate racemase-like | None |
| 2OG9 | 91786345 | 2,669 | 2,664 | 10 | 75 | 2,553 | Mandelate racemase-like | l-Talarate/galactarate dehydratase |
| 2OLA | 88195610 | 2,719 | 2,697 | 5 | 3 | 2,652 | Muconate cycloisomerase-like | o-Succinylbenzoate synthase |
| 2OO6 | 91778214 | 3,271 | 3,221 | 3 | 2 | 3,111 | Mandelate racemase-like | None |
| 2OKT | 57650581 | 2,723 | 2,705 | 5 | 3 | 2,664 | Muconate cycloisomerase-like | o-Succinylbenzoate synthase |
| 2OPJ | 72161814 | 2,562 | 1,855 | 19 | 31 | 1,712 | Mandelate racemase-like | o-Succinylbenzoate synthase |
| 2OX4 | 56552160 | 2,733 | 2,639 | 11 | 136 | 2,449 | Mandelate racemase-like | None |
| 2OZ3 | 67154209 | 2,743 | 2,656 | 38 | 25 | 2,567 | Mandelate racemase-like | None |
| 2OZ8 | 13475907 | 2,821 | 2,674 | 0 | 0 | 2,641 | Mandelate racemase-like | None |
| 2POI | 46136735 | 2,747 | 2,661 | 13 | 52 | 2561 | Mandelate racemase-like | None |
| 2OZT | 22294898 | 2,816 | 2,726 | 0 | 16 | 2,722 | Muconate cycloisomerase-like | o-Succinylbenzoate synthase |
| 2PCE | 83951697 | 2,693 | 2,683 | 1 | 16 | 2,635 | Muconate cycloisomerase-like | None |
| 2PGE | 51244103 | 2,779 | 2,767 | 1 | 19 | 2,768 | Muconate cycloisomerase-like | o-Succinylbenzoate synthase |
| 2PGW | 16263250 | 2,781 | 2,743 | 1 | 3 | 2,694 | Mandelate racemase-like | None |
| 2PMQ | 114764387 | 2,881 | 2,760 | 3 | 14 | 2,723 | Muconate cycloisomerase-like | None |
| 2POD | 53723090 | 2,745 | 2,732 | 12 | 97 | 2,585 | Mandelate racemase-like | Galactonate dehydratase |
| 2POZ | 13488170 | 2,861 | 2,836 | 1 | 162 | 2,687 | Mandelate racemase-like | None |
| 2PPG | 16262827 | 2,947 | 2,755 | 2 | 66 | 2,707 | Mandelate racemase-like | None |
| 2PS2 | 83774494 | 2,777 | 2,753 | 3 | 16 | 2,712 | Muconate cycloisomerase-like | None |
| 2QDE | 56478643 | 2,930 | 2,670 | 1 | 62 | 2,595 | Muconate cycloisomerase-like | None |
| 2QGY | 110347373 | 2,988 | 2,899 | 0 | 1 | 2,912 | Mandelate racemase-like | None |
| 2QQ6 | 108803396 | 3,238 | 3,216 | 0 | 201 | 3,081 | Mandelate racemase-like | Galactonate dehydratase |
| 2QYE | 83951695 | 3,128 | 3,121 | 0 | 21 | 3,110 | Muconate cycloisomerase-like | None |
| 3BJS | 6791043 | 3,261 | 2,897 | 4 | 82 | 2,810 | Mandelate racemase-like | None |
| 2QDD | 83951694 | 2,868 | 2,852 | 0 | 20 | 2,849 | Muconate cycloisomerase-like | o-Succinylbenzoate synthase |
| 3CAW | 42522147 | 2,220 | 2,139 | 0 | 0 | 2,137 | Muconate cycloisomerase-like | o-Succinylbenzoate synthase |
| 3CT2 | 70731221 | 3,483 | 2,771 | 84 | 77 | 2,667 | Muconate cycloisomerase-like | Muconate cycloisomerase |
| 3CYJ | 108805509 | 3,551 | 2,879 | 8 | 35 | 2,838 | Mandelate racemase-like | None |
| 3DDM | 33575875 | 3,603 | 3,576 | 6 | 27 | 3,591 | Mandelate racemase-like | None |
| 3BSM | 92115090 | 3,372 | 3,359 | 86 | 165 | 3,097 | Mannonate dehydratase-like | Mannonate dehydratase |
| Total (unique sequences) | 7,013 | 5,804 | 398 | 766 | 5,190 | |||
| Amidohydrolase superfamily | ||||||||
| 2GOK | 17742376 | 3,001 | 2,943 | 96 | 103 | 2,678 | Imidazolonepropionase-like | Imidazolonepropionase |
| 2OOD | 27378991 | 3,609 | 3,572 | 0 | 160 | 3,440 | Guanine deaminase-like | None |
| 2OOF | 83646866 | 3,588 | 3,578 | 142 | 154 | 3,270 | Imidazolonepropionase-like | Imidazolonepropionase |
| 2I5G | 9951721 | 569 | 448 | 28 | 50 | 340 | None | None |
| 2I9U | 15023121 | 3,386 | 3,363 | 5 | 96 | 3,198 | Newfam59 | None |
| 2ICS | 29342885 | 3,433 | 3,334 | 3 | 28 | 3,209 | Unknown18 | None |
| 2IMR | 9911007 | 3,790 | 3,502 | 1 | 3 | 3,498 | None | None |
| 2OGJ | 17741648 | 3,527 | 3,510 | 5 | 18 | 3,395 | Newfam71 | None |
| 2P9B | 23466009 | 3,319 | 3,302 | 2 | 37 | 3,230 | Unknown41 | None |
| 2PAJ | 91783796 | 3,264 | 3,252 | 4 | 116 | 3,128 | Unknown55 | None |
| 2QO1 | 13422863 | 460 | 263 | 35 | 14 | 172 | Uronate isomerase-like | Uronate isomerase |
| 2Q6B | 15615056 | 306 | 189 | 3 | 0 | 167 | Uronate isomerase-like | Uronate isomerase |
| 2QS8 | 114773165 | 3,508 | 3,497 | 15 | 144 | 3,280 | Unknown43 | None |
| 2QT3 | 32455889 | 3,723 | 3,693 | 1 | 49 | 3,606 | Unknown95 | None |
| 2RAG | 16126978 | 911 | 602 | 7 | 53 | 502 | Newfam32 | None |
| 2R8C | 4447959 | 3,649 | 3,632 | 19 | 195 | 3,359 | Unknown47 | None |
| 2I9U | 150231121 | 3,386 | 3,363 | 5 | 96 | 3,198 | Newfam59 | None |
| 2OOF | 83646866 | 3,588 | 3,578 | 142 | 154 | 3,270 | Imidazolonepropinase-like | Imidazolonepropionase |
| 3B40 | 9948434 | 1,149 | 656 | 16 | 34 | 504 | Newfam190 | None |
| 3CJP | 15896580 | 3,289 | 3,286 | 1 | 1,467 | 1,851 | Newfam63 | None |
| 3BE7 | 4436882 | 3,697 | 3,198 | 4 | 112 | 3,042 | Unknown42 | None |
| Total (unique sequences) | 12,101 | 11,628 | 302 | 2,429 | 8,912 | |||
Only one entry is shown for structures determined in different crystal forms or ligand binding states. An acceptable model is defined to be based on a significant PSI-BLAST E-value (0.0001) or a favorable GA341 model score (>0.7) [60]