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The Open Protein Structure Annotation Network
PDB Keyword
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2g40

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of hypothetical protein (6459694) from Deinococcus radiodurans at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 2g40 Target Id 357226
    Molecular Characteristics
    Source Deinococcus radiodurans r1
    Alias Ids TPS1376,6459694, PF02589, BIG_379, 289799 Molecular Weight 22619.64 Da.
    Residues 212 Isoelectric Point 5.52
    Sequence mttipstaeaklemlttinraiagsrpealppypvpaplsraeilhqfedrildygaaythvsaaelpg aiakalgnarrvivpagipapwltvgmdvlrdepplshaeldradavltgcavaisetgtiildhradq grralslipdfhicvvredqivqtvregveavaasvregrpltwlsggsatsdielvrvegvhgprrlq vivvg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.22
    Matthews' coefficent 1.80 Rfactor 0.178
    Waters 132 Solvent Content 29.30

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Gene DR_1909 from Deinococcus radiodurans encodes the NP_295632 protein that belongs to the DUF162 family (PF02589).

    2g40 shows a reasonably good structural alignment (3.2 Å over 87 residues, Z-score 3.4, 11% sequence id) with a transhydrogenase from Rhodospirillum rubrum (PDB id: 1u28). 2g40 shares some common features with the dIII and each of the two domains of the dI subunits of 1u28, such as a core parallel beta sheet flanked by alpha-helices on both sides, but a very different strand order and only partial topological similarity. 2g40 appears to be dimeric.

        

    To do: check whether NAD(P) can be docked onto 2g40. No visible GxGxxG motif.

    Top FFAS hits are:

      Score Template Links and tools %id First MTTIPSTAEAKLEMLTTINRAIAGSRPEALPPYPVPAPLSRAEILHQFEDRILDYGAAYTHVSAAELPGAIAKALGNARRVIVPAGIPAPWLTVGMDVLRDEPPLSHAELDRADAVLTGCAVAISETGTIILDHRADQGRRALSLIPDFHICVVREDQIVQTVREGVEAVAASVREGRPLTWLSGGSATSDIELVRVEGVHGPRRLQVIVVG Last
    1 -97.800 2g40_A mol:protein length:224 conserved hypothetical protein  ali model follow..  100  7 MTTIPSTAEAKLEMLTTINRAIAGSRPEALPPYPVPAPLSRAEILHQFEDRILDYGAAYTHVSAAELPGAIAKALGNARRVIVPAGIPAPWLTVGMDVLRDEPPLSHAELDRADAVLTGCAVAISETGTIILDHRADQGRRALSLIPDFHICVVREDQIVQTVREGVEAVAASVREGRPLTWLSGGSATSDIELVRVEGVHGPRRLQVIVVG 218
    2 -8.150 3brc_A mol:protein length:156 Conserved protein of unknown function  ali model follow..  12  21 .......................................DRSEEVEAIRKYIRSARRTVVPNWNAEKVDAINDVLRSFNLREAEHLQFNTNWADLTRMPAVTKALMALDISGADLVIARGRLGVPGSGSLLVIMDSRGRLLSAAMSPPHVI----REAVRSEMTHALERI.......................................... 152
    3 -6.620 2d74_B mol:protein length:148 Translation initiation factor 2 beta subunit  ali model follow..  12  32 .................................................................................................................................................VPGALVTIEGNKTIIENFKDIADALRDPQHLLKFLLREIATAGTLEGRRVVLQGRFTPYLIANKL.. 97
    4 -6.520 3szq_A mol:protein length:206 Aprataxin-like protein  ali model follow..  10  21 .....................................................................................................................SYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALCNYIKVGFHAGPSLHLHIMT 126
    5 -6.380 1nee_A mol:protein length:138 Probable translation initiation factor 2 beta  ali model follow..  12  30 .................................................................................................................................................VPKAYSVIQGNRTFIQNFREVADALRDPQHLLKFLLRELGTAGNLEGGRAILQGKFTHFLINERI.. 95
    6 -6.290 1byr_A mol:protein length:155 PROTEIN (ENDONUCLEASE)  ali model follow..  17 .........................................VLVLSAIDSAKTSIRMMAYSFTAPDIMKALVAAKKRGVDVKIVIDERGNTGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVD-NVTVETGSFNFTKAAETKNSENAVVIWNMPKLAESFLEHWQDR.......................................... 144
    7 -6.270 2ygo_A mol:protein length:188 WNT INHIBITORY FACTOR 1  ali model follow..  17  1 .............................................................................................................................ETGSLYLWIDAHQARVLIGF--EEDILIVSEGKMAPFTHDFRKAQQRMPAIPVNIHSMNFTWQAA...................... 63
    8 -6.230 2zkt_A mol:protein length:412 2,3-bisphosphoglycerate-independent phosphogl  ali model follow..  193 .........................................EEFVKKAQEVLEKHPINERRRKEGKPIANYLLIRGAGTYPNIPMKFTEQWKVKAAGVIAVALVKGVARAVGFDVYTPEGATGEYNTN-------MAKAKKAVELLKDYDFVFLHFKELIERADRMIGYILDHVDLEEVVIAI-----TGDHSTPCEVMNHSGDPVPLLIAG 367
    9 -6.020 2gel_A mol:protein length:231 Putative Gram negative resuscitation promotin  ali model follow..  25  2 ............................................................................................................RILAIDTATEACSVALWNNGTINAHFELCPREHTQRILP---------------VQEILAASGASLNEIDALAFGRGPSFTG-IGIGIAQGLALGANLPMIGVS 93
    10 -6.010 3r6m_A mol:protein length:213 YeaZ, resuscitation promoting factor  ali model follow..  18  3 ............................................................................................................KILAIDTATENCSVALLVNDQVISRSEVAPRDHTKKVLP---------------VDEVLKEAGLTLQDLDALAFGRGPSFTG-IGIGIAQGLAFGAELPMIGVS 94

     

    Top Dali hits are:

     

    No: Chain Z rmsd lali nres %id PDB Description

         1:  2g40-A 35.3  0.0  164   164  100 PDB  MOLECULE: CONSERVED HYPOTHETICAL PROTEIN;                            
       2:  1vb5-B  8.3  3.9  126   275   10 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B;                      
       3:  1vb5-A  8.3  4.0  126   274   10 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B;                      
       4:  3ecs-E  8.3  3.7  124   285   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
       5:  3a11-A  8.2  3.4  122   320   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
       6:  3ecs-G  8.2  3.7  125   284   12 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
       7:  3a11-B  8.1  3.4  124   322   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
       8:  3ecs-D  8.1  3.7  125   291   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
       9:  3a9c-A  8.0  3.4  122   320   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      10:  3ecs-H  8.0  3.8  127   285   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
      11:  3ecs-A  8.0  3.6  124   279   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
      12:  3ecs-C  7.9  3.7  125   294   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
      13:  3a11-C  7.9  3.3  120   317   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      14:  3vm6-C  7.9  3.8  124   321   10 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      15:  3vm6-A  7.9  3.8  124   321   10 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      16:  3vm6-B  7.9  3.8  124   321   10 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      17:  3ecs-B  7.9  3.8  126   281   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
      18:  3ecs-F  7.9  3.7  127   287   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B SUBUNIT               
      19:  3a9c-B  7.8  3.4  122   325   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      20:  3a9c-C  7.8  3.4  122   321   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      21:  3a9c-E  7.8  3.4  122   321   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      22:  3a9c-F  7.8  3.4  122   322   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      23:  3a11-F  7.8  3.5  123   319   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      24:  3a11-E  7.8  3.3  120   317   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      25:  3a9c-D  7.8  3.4  122   322   11 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      26:  3a11-D  7.8  3.3  120   320   12 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF-2B, DELTA SUBUN          
      27:  2yvk-D  7.5  4.0  125   349   10 PDB  MOLECULE: METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE;                    
      28:  2yrf-A  7.5  4.1  125   340   10 PDB  MOLECULE: METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE;                    
      29:  1t5o-D  7.5  3.0  120   340    9 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF2B, SUBUNIT DELT          
      30:  1t5o-C  7.5  3.0  121   340   10 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF2B, SUBUNIT DELT          
      31:  2yvk-A  7.4  4.0  125   349   10 PDB  MOLECULE: METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE;                    
      32:  2yrf-B  7.4  4.2  127   341   10 PDB  MOLECULE: METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE;                    
      33:  1t5o-B  7.4  3.0  121   340   10 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF2B, SUBUNIT DELT          
      34:  1t5o-A  7.3  3.0  120   340    9 PDB  MOLECULE: TRANSLATION INITIATION FACTOR EIF2B, SUBUNIT DELT          
      35:  2yvk-C  7.3  4.2  127   349   10 PDB  MOLECULE: METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE;                    
      36:  2a0u-B  7.3  3.9  126   367    9 PDB  MOLECULE: INITIATION FACTOR 2B;                                      
      37:  1t9k-C  7.1  4.2  127   342   14 PDB  MOLECULE: PROBABLE METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE;           
      38:  1t9k-D  7.1  4.2  127   342   15 PDB  MOLECULE: PROBABLE METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE;           
      39:  2a0u-A  6.9  3.9  126   374    9 PDB  MOLECULE: INITIATION FACTOR 2B;                                      
      40:  1lk5-A  6.9  3.3  121   229   12 PDB  MOLECULE: D-RIBOSE-5-PHOSPHATE ISOMERASE;                            
      41:  1lk7-A  6.9  3.3  121   229   12 PDB  MOLECULE: D-RIBOSE-5-PHOSPHATE ISOMERASE;                            
      42:  4io1-B  6.9  3.1  121   215   14 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      43:  4gmk-B  6.8  3.0  118   224   13 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      44:  3hhe-A  6.7  3.2  119   233   12 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      45:  3hhe-B  6.7  3.4  120   233   11 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      46:  3l7o-A  6.7  3.2  116   221   16 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      47:  3uw1-A  6.7  3.3  120   232    9 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      48:  4gmk-A  6.6  3.3  118   227   11 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      49:  3l7o-B  6.6  3.3  120   224   16 PDB  MOLECULE: RIBOSE-5-PHOSPHATE ISOMERASE A;                            
      50:  1o8b-B  6.5  3.2  116   212   11 PDB  MOLECULE: RIBOSE 5-PHOSPHATE ISOMERASE;                              
    

     

    Its function is likely related to lactate utilization, as it is similar to lactate utilization protein C in the sequence alignment. The following is an alignment of 2g40 with Lactate utilization protein C from Bacilus cereus (strain 03BB102).

     

    LUTC_BACC3      MTGLIQNRDSFLDNIAKELGRTRKTDGVERPVWKNNVNKETLKDYSQEELLEVFKNQCTN
    2G40            MTTIPSTAEAKLEMLTTINRAIAGSRPEALPPYP------VPAPLSRAEILHQFEDRILD
                    ** : .. :: *: ::.       :     * :       .    *: *:*. *:::  :
    
    LUTC_BACC3      IHTTVVETTNDRLREDIQKVIVENGGGPIMLSADERFDSYGLTSLFKEELPKQNVEVNVW
    2G40            YGAAYTHVSAAELPGAIAKALGNARRVIVPAGIPAPWLTVGMDVLRDEPP----------
                      :: ...:  .*   * *.: :     :  .    : : *:  * .*            
    
    LUTC_BACC3      DPEKKEENMRIAERANIGIAFSDYTLAESGTIVVQSHKGQGR-SLHFLPTVYFAIIPRET
    2G40            ------LSHAELDRADAVLTGCAVAISETGTIILDHRADQGRRALSLIPDFHICVVREDQ
                           .    :**:  :: .  :::*:***::: : .*** :* ::* .::.:: .: 
    
    LUTC_BACC3      LVPRITQAVQDMNTRVENGEEVASCINFITGPSNSADIEMNLVVGVHGPLKAVYFIV-
    2G40            IVQTVREGVEAVAASVREG----RPLTWLSGGSATSDIELVRVEGVHGPRRLQVIVVG
                    :*  : :.*: : : *.:*      :.:::* * ::***:  * ***** :   ::* 
    

     

    The C-terminus is highly conserved:

     

    2G40_HMM_plot.png

     

    The LutABC operons were highly conserved and were found in a wide variety of gram-positive and gram-negative bacteria [Ref]. Models for LutA-LutB-LutC-mediated oxidation of l-lactate and for regulation of the operon [Ref]:

     

    Ligand Summary



    References

    Reviews

    References

     

    1. (No Results)

       


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