Current revision

Structural annotation of Rv2753c (dihydrodipicolinate synthase)
Name
Dihydrodipicolinate Synthase
Identifiers
Swiss Prot	P63945
Genbank	888289
PDB	1XXX
Chemical data
Formula	?
Mol. wt.	30,858 Da
Pharmacokinetic data
Bioavailability	?
Solubility	?
Isoelectric-Point	5.57

[edit] General

dapA catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate.

L-aspartate 4-semialdehyde + pyruvate = dihydrodipicolinate + 2H₂O.

This protein is eesential for optimal growth of M.tb and found in the cytoplasm as predicted by the WoLFPSORT and Subloc Server. HMMpfam found one domain PF00701 and has Helix Turn Helix secondary structure.

[edit] Amino Acid Sequence of Rv2753c

>Rv2753c, TB.seq 3066222:3067121 MW:30827 VTTVGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDR ARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRA LASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKI NIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR

[edit] Tertiary Structure

This protein structure is available in PDB and having code 1XXX

Detail information available at OCA browser 1XXX

Discussion on this protein available at TopSCAN 1XXX

[edit] Structure Prediction

As information is available so we are not applying protein structure prediction method

[edit] Structure Classification

Protein: Dihydrodipicolinate synthase from Mycobacterium tuberculosis SCOP_1XXX

Structural classification of 1XXX as per CATH CATH_1XXX

[edit] Secondray Structure

Secondary structure of this protein (assigned using DSSP) 1XXX.DSSP

[edit] Secondary Structure Prediction

We are not applying structure prediction method as structure is available

[edit] Related Publications

Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis. Biochem J. 2008 Apr 15;411(2):351-60

Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase. Protein Sci. 2008 Dec;17(12):2080-90. Epub 2008 Sep 11

@@ Line 7: / Line 7: @@
 | Genbank          = 888289
 | PDB         = 1XXX
-| DrugBank          =
-| chemical_formula  =
 | molecular_weight  = 30,858 Da
 | solubility        =
@@ Line 19: / Line 17: @@
 This protein is eesential for optimal growth of M.tb and found in the cytoplasm as predicted by the [http://wolfpsort.org/aboutWoLF_PSORT.html.en WoLFPSORT] and [http://www.biohealthbase.org/brc/localizationPrograms.do?decorator=mycobacterium  Subloc] Server. HMMpfam found one domain PF00701 and has Helix Turn Helix secondary structure.
-=Human Homologue Blast Result=
+=Amino Acid Sequence of Rv2753c=
+>Rv2753c, TB.seq  3066222:3067121 MW:30827
+VTTVGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDR
+ARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRA
+LASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKI
+NIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR
-<table border='1'><tr>
+=Tertiary Structure=
+This protein structure is available in PDB and having code [http://www.rcsb.org/pdb/explore/explore.do?structureId=1XXX 1XXX]
-<td>subject ids</td><td>% identity</td><td>% positives</td><td>alignment length</td><td> evalue</td></tr>
+Detail information available at OCA browser [http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocashort?id=1XXX 1XXX]
-<tr><td>sp|Q9BXD5</td><td>	28</td><td>	46.33</td><td>	300</td><td>	3.00E-023</td></tr>
+Discussion on this protein available at TopSCAN [http://www.topsan.org/Proteins/XMTB/1xxx 1XXX]
-<tr><td>sp|Q86XE5</td><td>	26.57</td><td>	46.15</td><td>	286</td><td>	4.00E-022</td></tr>
+==Structure Prediction==
+As information is available so we are not applying protein structure prediction method
-<tr><td>sp|Q9UG63</td><td>	26.49</td><td>	37.75</td><td>	151</td><td>	0.45</td></tr>
+= Structure Classification =
+Protein: Dihydrodipicolinate synthase from Mycobacterium tuberculosis [http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.b.bb.b.bc.html SCOP_1XXX]
-<tr><td>sp|O14556</td><td>	22.09</td><td>	50</td><td>	86</td><td>	2</td></tr>
+Structural classification of 1XXX as per CATH [http://www.cathdb.info/pdb/1xxx CATH_1XXX]
-<tr><td>sp|Q7Z7B0</td><td>	27.69</td><td>	44.62</td><td>	65</td><td>	2.7</td></tr></table>
+==Secondray Structure==
-=Antigens=
+Secondary structure of this protein (assigned using DSSP) [ftp://ftp.cmbi.kun.nl/pub/molbio/data/dssp/1xxx.dssp 1XXX.DSSP]
-No Hit Found in AntigenDB Database.<br>
+==Secondary Structure Prediction==
+We are not applying structure prediction method as structure is available
+=Related Publications=
+Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis. [http://www.ncbi.nlm.nih.gov/pubmed/18062777?dopt=Abstract Biochem J. 2008 Apr 15;411(2):351-60]
-No Hit Found in IEDB Database.<br>
+Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2590918/?tool=pubmed Protein Sci. 2008 Dec;17(12):2080-90. Epub 2008 Sep 11]
-No Hit Found in MHCBN Database.<br>
-No Hit Found in BciPep Database.<br>
-=Haptens=
-=Epitopes=
-===B-Cell Epitopes===
-===MHC class I restricted T cell epitopes===
-===CTL Epitopes===
-=MHC Binder=
-===Class-I Binder===
-Result predicted by [http://www.imtech.res.in/raghava/nhlapred/comp.html nhlapred]
-<table border='1'>
-<tr><td>Epitope</td><td>No of Alleles
-</td></tr><tr><td>
-VPIEPDTIR </td><td>      15
-</td></tr><tr><td>
-TPFSGDGSL  </td><td>     14
-</td></tr><tr><td>
-TLSKAGLRL  </td><td>     13
-</td></tr><tr><td>
-IEPDTIRAL </td><td>      13
-</td></tr><tr><td>
-GTYDTAHSI  </td><td>     13
-</td></tr><tr><td>
-DDALNLPWL </td><td>      11
-</td></tr><tr><td>
-GFISVIAHL   </td><td>    10
-</td></tr><tr><td>
-GATGFISVI   </td><td>    10
-</td></tr><tr><td>
-ATPEQIDAL  </td><td>     10
-</td></tr><tr><td>
-YDTAHSIRL  </td><td>     9
-</td></tr><tr><td>
-GDIATARKI  </td><td>     9
-</td></tr><tr><td>
-AVLEAVGDR </td><td>      9
-</td></tr><tr><td>
-ASHPNIVGV  </td><td>     9
-</td></tr><tr><td>
-QRGLQAHFT  </td><td>     7
-</td></tr><tr><td>
-GLQAHFTAV   </td><td>    7
-</td></tr><tr><td>
-AVGDRARVI   </td><td>    7
-</td></tr><tr><td>
-YSGDDALNL   </td><td>    6
-</td></tr><tr><td>
-VGFDVAARL   </td><td>    6
-</td></tr><tr><td>
-QLRELLSAF  </td><td>     6
-</td></tr><tr><td>
-TAVADATEL  </td><td>     5
-</td></tr><tr><td>
-TAARLANHL  </td><td>     5
-</td></tr><tr><td>
-LLRAVLEAV   </td><td>    5
-</td></tr><tr><td>
-GEKIELLRA  </td><td>     5
-</td></tr><tr><td>
-DTATAARLA   </td><td>    5
-</td></tr><tr><td>
-AAGQLRELL  </td><td>     5
-</td></tr><tr><td>
-TDGEKIELL   </td><td>    4
-</td></tr><tr><td>
-QAHFTAVAD </td><td>      4
-</td></tr><tr><td>
-MSRLGGVTL  </td><td>     4
-</td></tr><tr><td>
-LDTATAARL  </td><td>     4
-</td></tr><tr><td>
-HPNIVGVKD  </td><td>     4
-</td></tr><tr><td>
-GVKDAKADL   </td><td>    4
-</td></tr><tr><td>
-DGEKIELLR   </td><td>    4
-</td></tr><tr><td>
-KIELLRAVL   </td><td>    3
-</td></tr><tr><td>
-HSIRLAKAC   </td><td>    3
-</td></tr><tr><td>
-GSGDIATAR   </td><td>    3
-</td></tr><tr><td>
-AHLAAGQLR  </td><td>     3
-</td></tr><tr><td>
-PTTTDGEKI  </td><td>     2
-</td></tr><tr><td>
-IAHLAAGQL  </td><td>     2
-</td></tr><tr><td>
-DLHSGAQIM   </td></tr><tr><td>    2
-</td></tr></table>
-Result predicted by [http://tools.immuneepitope.org/analyze/html/mhc_processing.html IEDB]
-<table border='1'><tr><td>
-Epitope</td><td> No of Alleles
-</td></tr><tr><td>
-RVIAGAGTY </td><td>      12
-</td></tr><tr><td>
-IMADTGLAY  </td><td>     11
-</td></tr><tr><td>
-MADTGLAYY  </td><td>     7
-</td></tr><tr><td>
-GLQAHFTAV </td><td>      7
-</td></tr><tr><td>
-ATELPMLLY  </td><td>     6
-</td></tr><tr><td>
-ALASHPNIV  </td><td>     6
-</td></tr><tr><td>
-GTYDTAHSI  </td><td>     5
-</td></tr><tr><td>
-GLLVVTPYY  </td><td>     5
-</td></tr><tr><td>
-MSRLGGVTL  </td><td>     4
-</td></tr><tr><td>
-LLRAVLEAV  </td><td>     4
-</td></tr><tr><td>
-WLAMGATGF  </td><td>     3
-</td></tr><tr><td>
-QLRELLSAF  </td><td>     3
-</td></tr><tr><td>
-RALASHPNI  </td><td>     2
-</td></tr><tr><td>
-LLTAMVTPF  </td><td>     2
-</td></tr><tr><td>
-KINIAVAPL  </td><td>     2
-</td></tr><tr><td>
-GFISVIAHL  </td><td>     2
-</td></tr></table>
-===Class-II Binder===
-=Alergen Protein=
-Non Allergen Predicted by AlgPred Server
-=External Links=
 [[Category:C2D]]
 [[Category:Mtb Station]]

Structural annotation of Rv2753c (dihydrodipicolinate synthase)

From DrugPedia: A Wikipedia for Drug discovery

Current revision

Contents

[edit] General

[edit] Amino Acid Sequence of Rv2753c

[edit] Tertiary Structure

[edit] Structure Prediction

[edit] Structure Classification

[edit] Secondray Structure

[edit] Secondary Structure Prediction

[edit] Related Publications

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