Structure of E. coli DnaC helicase loader

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Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.
Templates for 2008 Homology Modeling of E. coli DnaC (245 amino acids)
Name PDB Code (Resolution) Released Length (amino acids)a Template alignment lengtha: range (%) Target alignment lengtha: range (%) Aligned Sequence Identity Expectations Swiss Model Result
Putative Primosome Component Streptococcus Pyogenes 2qgz (2.4 Å) Jul 24 2007 183 (308) 174:107-292 (95%) [sm] (183): 55-237 (75%) [sm] 18.6% [sm]; 19.7% [tdb] 3.4e-28 [sm]; 0.00027 [tdb]; >10 [pdbB]; 0.0028 [pdbF] DnaC modeled from 2qgz chain A
DnaC helicase loader Aquifex aeolicus 3ec2 (2.7 Å) Nov 25 2008 175 (180) 174: 6-179 (95%) [pdbB] (163): 68-230 (67%) [pdbB] 23.5% [pdbB] 0.00059 [pdbB] "Alignment is not good enough for Modelling"

Sources: Swiss-Model [sm]; targetdb.pdb.org [tdb]; pdb.org using a BLAST search [pdbB], or a FASTA search [pdbF].
(a) Lengths not in parentheses are for crystallographic results, and are counts of amino acids with coordinates; they exclude disordered residues ("gaps" in the model). Lengths in parentheses are for the target sequence of DnaC, or sequences of the crystallized protein (from SEQRES in the PDB file).

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).

                                                 |     | |  |     ||
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 

                            |         | ||   ||     | |              |
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 

                                   ||   |  | ||                |
TARGET    144   DTFRNSGTSE EQLLNDLSNV DLLVIDEIGV QTESKYEKVI INQIVDRRSS
2qgzA     198   naiske---- --eidavknv pvlilddiga vrde-----v lqvilqyrml
                   /\                          / \
TARGET                         hhh     ssssss               hhhhhhhhhh
2qgzA                        hh   h    ssssss               hhhhhhhhhh

                   |     |                 ||| |  |               |
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         

ConSurf Coloring Script

For an explanation of the evolutionary conservation results, see above. The script below is from the 2012 analysis[4]. It can be run in Jmol to color the amino acids of DnaC by evolutionary conservation. CON10 marks insufficient data. CON9 is the highest level of conservation, and CON1 is the lowest (most variable).

select all
color [200,200,200]

select PHE57
color [255,255,150]
spacefill
define CON10 selected

select ILE62, ASN73, GLY106, GLY109, THR110, GLY111, LYS112, HIS114, LEU115
select selected or ALA116, ALA118, GLU153, LEU165, LEU166, ASP169, GLU170
select selected or GLY172, ASP189, ARG191, ASN203, ARG216, ASP219, ARG220
select selected or TRP233, SER235, ARG237
color [160,37,96]
spacefill
define CON9 selected

select ARG55, SER60, GLY61, LEU65, PHE71, TYR74, ALA84, VAL92, PHE95, ASN113
select selected or ILE119, LEU123, VAL130, THR134, THR145, VAL163, ILE168
select selected or GLN174, SER177, GLU180, ILE187, SER192, PRO197, THR198
select selected or THR202, GLY214, MET221, SER226, PHE231
color [240,125,171]
spacefill
define CON8 selected

select HIS66, GLN81, PHE102, VAL135, SER140, LYS143, SER152, LEU156, ASP164
select selected or VAL167, ILE171, ILE184, ASN185, VAL188, GLY199, LEU213
color [250,201,222]
spacefill
define CON7 selected

select THR56, ARG59, CYS69, SER70, ALA88, TYR91, ILE99, SER101, PHE104, SER105
select selected or ALA117, CYS120, ASN121, LEU124, GLY127, SER129, ILE133
select selected or ALA136, ASP137, ILE138, MET139, PHE146, ILE183, GLN186
select selected or ARG190, SER193, MET200, LEU201, SER204, LEU223, GLY224
select selected or ASN225, VAL229
color [252,237,244]
spacefill
define CON6 selected

select ASN58, ARG63, ASN68, VAL76, GLY80, LEU85, ASN98, ALA100, ILE103, LEU131
select selected or MET142, LEU157, LEU160, SER161, VAL182, SER194, ASN205
select selected or MET209, VAL217, TYR236
color [255,255,255]
spacefill
define CON5 selected

select ARG89, GLU94, PRO108, SER149, GLU154, LYS178, TYR179, LYS181, ARG196
select selected or GLU215, LEU227
color [234,255,255]
spacefill
define CON4 selected

select PRO64, GLN67, GLU72, CYS78, MET82, ILE132, GLU176, GLU208, ASN232
color [215,255,255]
spacefill
define CON3 selected

select GLN90, ARG126, ALA141, VAL173, LYS195
color [140,255,255]
spacefill
define CON2 selected

select ARG75, GLU77, GLU79, ASN83, SER86, LYS87, GLU93, ASP96, GLY97, LYS107
select selected or GLU122, LEU125, LYS128, ASP144, ARG147, ASN148, GLY150
select selected or THR151, GLN155, ASN158, ASP159, ASN162, THR175, MET206
select selected or GLU207, THR210, LYS211, LEU212, MET218, ARG222, TRP228
select selected or ILE230, ASP234
color [16,200,209]
spacefill
define CON1 selected

Notes & References

  1. A model was created in 2008 by Swiss-Model using its totally automated first approach mode with template 2qgz. In 2012, Swiss-Model's automated mode chose a different template, 3ecc, and created a similar model.
  2. Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22,195-201. Free full text. Server: swissmodel.expasy.org
  3. 3.0 3.1 In December, 2008, Swiss-Model deemed the sequence alignment of E. coli DnaC with A. aeolicus DnaC to be too unreliable to permit using the 3ec2 structure of the latter as a template for homology modeling of E. coli DnaC.
  4. 4.0 4.1 4.2 In the 2012 analysis, ConSurf found 47 unique sequences in Clean Uniprot. The MSA had an average pairwise distance of 0.98.
  5. In 2008, ConSurf found only 10 sequences in SwissProt, with an average pairwise distance (APD), in the multiple sequence alignment, of 1.6. The run shown here used 100 sequences from Uniprot, with an APD of 1.4.
  6. ConSurf result using 50 sequences from Uniprot, with an average pairwise distance in the multiple sequence alignment of 1.6.
  7. Not clear to User:Eric Martz in December, 2008.
  8. Registration refers to the positioning of amino acids along the backbone of the homology model. Amino acids are "in register" when correctly positioned. The sequence of the target protein (DnaC) can be thought of as sliding along the template backbone, as a consequence of the process of sequence alignment (or threading). The correct registration will be known only when an empirical crystallographic structure becomes available for DnaC.
  9. The structural alignment of 2qgz with 3ec2 was performed with the Magic Fit function of DeepView version 3.6beta2. 2qgz 115-259 aligned with 3ec2 42-185 (3 gaps in 3ec2's alignment: 128-9, 134-5, 155-9). 135 alpha carbons were aligned with RMS 2.76 Å. The sequence identity between 2qgz and 3ec2 is 28% over the 185 amino acid length of the shorter, 3ec2. Magic Fit is a sequence-alignment-guided structural alignment (see Structural alignment tools).
  10. Structural alignment done with DeepView 3.6b3 using Magic Fit of carbon alphas.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Alexander Berchansky, David Canner, Michal Harel

DOI: http://dx.doi.org/10.14576/333957.1802412 (?)
Citation: Martz E, Canner D, Harel M, Berchansky A, 2013, "Structure of E. coli DnaC helicase loader", Proteopedia, DOI: http://dx.doi.org/10.14576/333957.1802412
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