User:Eric Martz/Sandbox 6
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Homology Model of DnaCHomology Model of DnaC
The following sequence was provided for DnaC from E. coli:
MKNVGDLMQR LQKMMPAHIK PAFKTGEELL AWQKEQGAIR SAALERENRA
MKMQRTFNRS GIRPLHQNCS FENYRVECEG QMNALSKARQ YVEEFDGNIA
SFIFSGKPGT GKNHLAAAIC NELLLRGKSV LIITVADIMS AMKDTFRNSG
TSEEQLLNDL SNVDLLVIDE IGVQTESKYE KVIINQIVDR RSSSKRPTGM
LTNSNMEEMT KLLGERVMDR MRLGNSLWVI FNWDSYRSRV TGKEY
This sequence (245 amino acids) was submitted to Swiss Model, which generated the homology model shown here () using 2qgz chain A as a template, which has 18.6% sequence identity. Apparently Swiss Model used predicted secondary structure to help in the sequence alignment, but details are not clear to me. The homology model represents residues 55-237 (183 residues representing 75% of dnaC), shown in boldface in the above sequence. Because of the low sequence identity, this model may well contain major errors, or even be wholly incorrect.
Swiss Model has apparently used the temperature value field in the PDB file to indicate regions that are highly unreliable, namely the regions that are red when the model is . These regions are shown as translucent white in the initial scene (using the Jmol command select temperature >50). The uncertainty in three of these regions is explained by gaps in the template model (see below). Although the details of these regions are even more uncertain than other regions, it seems likely that these loops are on the surface, if the homology model turns out to be substantially correct.
Evolutionary Conservation in the Homology ModelEvolutionary Conservation in the Homology Model
The evolutionary conservation pattern, revealed by ConSurf, is quite interesting, showing .[1]
Homology Model in FirstGlanceHomology Model in FirstGlance
In order to find specific residues, or see charge distribution or other aspects of this homology model, please View The DnaC Homology Model in FirstGlance in Jmol
Structural Alignment with Closest Hit at PDBStructural Alignment with Closest Hit at PDB
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When the PDB is searched with the dnaC sequence, the closest hit is 39% identity with residues 9-63 of chain A of replication factor C (2CHG), which align with 72-124 of dnaC. When the above homology model of dnaC (made with template 2QGZ) is structurally aligned with residues 9-63 of 2CHG[2], 43 alpha carbons (out of 54) aligned with RMS deviation 2.3 Å. Residues 21-63 of 2CHG aligned with residues 80-124 of the dnaC homology model. (Non-aligned portions are pastel.) This result adds some confidence to the homology model, since the structural alignment of 2CHG:A21-63 occurred in the same range as the sequence alignment (which was 72-124 in dnaC).
Crystal Structure of DnaC Is "In The Pipeline"Crystal Structure of DnaC Is "In The Pipeline"
A sequence-based search at the international Structural Genomics TargetDB reveals that the closest completed structure is 2QGZ, the one chosen by SwissModel as a template. A number of crystal and NMR structures have sequence identities up to 37% but over shorter stretches, and with higher E values.
Diffraction data have been obtained (but the solved structure not yet deposited) for a Listeria monocytogenes sequence of 307 residues, pI 5.2, with an E value of 1.6e-05, though only 21% sequence identity. Diffraction-quality crystals (but not yet diffraction data) have not been obtained for any sequence with such a low E value.
E. coli dnaC (245 residues, pI 9.4) has been crystallized by RIKEN Structural Genomics Initiative (Japan), but the crystals may not be of diffraction quality. It has been cloned, expressed as a soluble protein, and purified (but not yet crystallized) by 3 Structural Genomics Groups (RIKEN Structural Genomics Initiative (Japan), Montreal-Kingston Bacterial Structural Genomics Initiative, Midwest Center for Structural Genomics), as have several proteins with >40% sequence identity. So there is reason for optimism that either a crystal structure, or a more suitable template for homology modeling, will be forthcoming soon. One might consider contacting the groups who have reported purification of dnaC to inquire about progress, and possibly request priority for dnaC.
Gaps in the Template ModelGaps in the Template Model
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The template was 2QGZ (). The portion of the template used was Glu107-Arg300. Only the amino-terminal 6 residues were not used as template (translucent). Note that there are in this segment of the template that lack coordinates due to disorder in the crystal (marked with spacefilled alpha-carbon atoms).
The missing loops are 202-205 (NGSV), 226-231 (EQATSW), and 268-275 (TIKGSDET). These gaps, which occur between the residues marked /\ below, were apparently ignored in making the model, which has a continuous main chain.
Below is the alignment produced by Swiss Model, used in making the 3D model. Vertical bars for identity were inserted by hand (I may have missed some).
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TARGET 55 R TFNRSGIRPL HQNCSFENYR VECEGQMNAL SKARQYVEEF
2qgzA 100 qkqaais--e riqlvslpks yrhihlsdid vnnasrmeaf saildfveqy
TARGET sssss h h hhhhhhh hhhhhhhhh
2qgzA hhh h sss h h hhhhhhh hhhhhhhhh
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TARGET 96 DGN-IASFIF SGKPGTGKNH LAAAICNELL L-RGKSVLII TVADIMSAMK
2qgzA 148 psaeqkglyl ygdmgigksy llaamahels ekkgvsttll hfpsfaidvk
TARGET ssss ss hhh hhhhhhhhhh h h ssss sshhhhhhh
2qgzA ssss ss hhh hhhhhhhhhh hh ssss sshhhhhhh
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TARGET 144 DTFRNSGTSE EQLLNDLSNV DLLVIDEIGV QTESKYEKVI INQIVDRRSS
2qgzA 198 naiske---- --eidavknv pvlilddiga vrde-----v lqvilqyrml
/\ / \
TARGET hhh ssssss hhhhhhhhhh
2qgzA hh h ssssss hhhhhhhhhh
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TARGET 194 SKRPTGMLTN SNMEEMTKLL ---GERVMDR MRLGNSLWVI FNWDSYR
2qgzA 247 eelptfftsn ysfadlerkw awqakrvmer vr-ylarefh leganrr-
/\
TARGET h ssssss hhhhh hhhh hh ssssss s
2qgzA h ssssss hhhh hhhh hh hh ssss s
Below is the sequence with ATOM records (coordinates) from 2QGZ, numbered 100-300, showing the gaps as "...". This sequence listing was used to locate the positions marked /\ above.
1 .......... .......... .......... .......... .......... 51 .......... .......... .......... .......... .........Q 101 KQAAISERIQ LVSLPKSYRH IHLSDIDVNN ASRMEAFSAI LDFVEQYPSA 151 EQKGLYLYGD MGIGKSYLLA AMAHELSEKK GVSTTLLHFP SFAIDVKNAI 201 S....KEEID AVKNVPVLIL DDIGA..... .VRDEVLQVI LQYRMLEELP 251 TFFTSNYSFA DLERKWA... .....WQAKR VMERVRYLAR EFHLEGANRR
(Copied from Protein Explorer's sequence display.)
Below is the alignment of full-length dnaC with 2QGZ according to TargetDB (see above). Note that the 2QGZ structure begins at residue 100, and so the homology model begins with residue 55 of dnaC, indicated with > below.
ID: DR58 Center: NESGC
E-value: 0.00028 Identity: 19.737%
10 20 30
Query MKNVGDLMQRLQKMMPAHIKPAFKTGEELLAWQKEQGA
Q+ Q P++I +++ + + +
Subjct EVASFISQHHLSQEQINLSLSKFNQFLVERQKYQLKDPSYIAKGYQPILAMNEGYADVSY
40 50 60 70 80 90
40 50 > 60 70 80 90
Query IRSAALERENRAMKMQRTFNRSGIRPLHQNCSFENYRVECEGQMNALSKARQYVEEF-DG
+++ L + ++ +++ ++ ++ +++ + + V+ ++M+A+S ++VE++ ++
Subjct LETKELVEAQKQAAISERIQLVSLPKSYRHIHLSDIDVNNASRMEAFSAILDFVEQYPSA
100 110 120 130 140 150
100 110 120 130 140 150
Query NIASFIFSGKPGTGKNHLAAAICNELLLR-GKSVLIITVADIMSAMKDTFRNSGTSEEQL
+ ++ + G G GK++L AA+ +EL + G S+ ++ ++ +K+++ N++++EE
Subjct EQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFAIDVKNAISNGSVKEE--
160 170 180 190 200
160 170 180 190 200 210
Query LNDLSNVDLLVIDEIGV-QTESKYEKVIINQIVDRRSSSKRPTGMLTNSNMEEMTK----
++ ++NV +L++D+IG+ Q+ S + +++ I++ R + PT + +N ++ ++ +
Subjct IDAVKNVPVLILDDIGAEQATSWVRDEVLQVILQYRMLEELPTFFTSNYSFADLERKWAT
210 220 230 240 250 260
220 230 240
Query LLG-------ERVMDRMRLGNSLWVIFNWDSYRSRVTGKEY
+ G +RVM+R+R
Subjct IKGSDETWQAKRVMERVRYLAREFHLEGANRR
270 280 290 300
NotesNotes
- ↑ ConSurf found only 10 sequences in SwissProt, with an Average Pairwise Distance of 1.6. The run shown here used 100 sequences from Uniprot, with an APD of 1.4.
- ↑ Structural alignment done with DeepView 3.6b3 using Magic Fit of carbon alphas.