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PDBsum entry 1nxj

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protein ligands Protein-protein interface(s) links
Unknown function PDB id
1nxj
Jmol
Contents
Protein chains
156 a.a. *
Ligands
GLV ×3
TLA ×3
Waters ×276
* Residue conservation analysis
PDB id:
1nxj
Name: Unknown function
Title: Structure of rv3853 from mycobacterium tuberculosis
Structure: Probable s-adenosylmethionine:2- demethylmenaquinone methyltransferase. Chain: a, b, c. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: meng. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.190     R-free:   0.215
Authors: J.M.Johnston,V.L.Arcus,E.N.Baker,Tb Structural Genomics Consortium (Tbsgc)
Key ref: J.M.Johnston et al. (2003). Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis. J Bacteriol, 185, 4057-4065. PubMed id: 12837779
Date:
10-Feb-03     Release date:   29-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P9WGY2  (RRAAH_MYCTO) -  Putative regulator of ribonuclease activity
Seq:
Struc:
157 a.a.
156 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.4.1.1.3  - Oxaloacetate decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Oxaloacetate = pyruvate + CO2
Oxaloacetate
= pyruvate
+ CO(2)
      Cofactor: Biotin; Sodium or manganese
Biotin
Sodium
or manganese
   Enzyme class 3: E.C.4.1.3.17  - 4-hydroxy-4-methyl-2-oxoglutarate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate
2. 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = oxaloacetate + pyruvate
4-hydroxy-4-methyl-2-oxoglutarate
= 2 × pyruvate
2-hydroxy-4-oxobutane-1,2,4-tricarboxylate
= oxaloacetate
+ pyruvate
      Cofactor: Divalent cation
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     ribonuclease inhibitor activity     3 terms  

 

 
    reference    
 
 
J Bacteriol 185:4057-4065 (2003)
PubMed id: 12837779  
 
 
Crystal structure of a putative methyltransferase from Mycobacterium tuberculosis: misannotation of a genome clarified by protein structural analysis.
J.M.Johnston, V.L.Arcus, C.J.Morton, M.W.Parker, E.N.Baker.
 
  ABSTRACT  
 
Bioinformatic analyses of whole genome sequences highlight the problem of identifying the biochemical and cellular functions of many gene products that are at present uncharacterized. The open reading frame Rv3853 from Mycobacterium tuberculosis has been annotated as menG and assumed to encode an S-adenosylmethionine (SAM)-dependent methyltransferase that catalyzes the final step in menaquinone biosynthesis. The Rv3853 gene product has been expressed, refolded, purified, and crystallized in the context of a structural genomics program. Its crystal structure has been determined by isomorphous replacement and refined at 1.9 A resolution to an R factor of 19.0% and R(free) of 22.0%. The structure strongly suggests that this protein is not a SAM-dependent methyltransferase and that the gene has been misannotated in this and other genomes that contain homologs. The protein forms a tightly associated, disk-like trimer. The monomer fold is unlike that of any known SAM-dependent methyltransferase, most closely resembling the phosphohistidine domains of several phosphotransfer systems. Attempts to bind cofactor and substrate molecules have been unsuccessful, but two adventitiously bound small-molecule ligands, modeled as tartrate and glyoxalate, are present on each monomer. These may point to biologically relevant binding sites but do not suggest a function. In silico screening indicates a range of ligands that could occupy these and other sites. The nature of these ligands, coupled with the location of binding sites on the trimer, suggests that proteins of the Rv3853 family, which are distributed throughout microbial and plant species, may be part of a larger assembly binding to nucleic acids or proteins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21443791 N.E.Arenas, L.M.Salazar, C.Y.Soto, C.Vizcaíno, M.E.Patarroyo, M.A.Patarroyo, and A.Gómez (2011).
Molecular modeling and in silico characterization of Mycobacterium tuberculosis TlyA: possible misannotation of this tubercle bacilli-hemolysin.
  BMC Struct Biol, 11, 16.  
20363939 H.A.Watkins, and E.N.Baker (2010).
Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.
  J Bacteriol, 192, 2878-2886.
PDB code: 3hst
21063756 J.Tang, M.Luo, S.Niu, H.Zhou, X.Cai, W.Zhang, Y.Hu, Y.Yin, A.Huang, and D.Wang (2010).
The crystal structure of hexamer RraA from Pseudomonas aeruginosa reveals six conserved protein-protein interaction sites.
  Protein J, 29, 583-590.  
20106955 M.W.Górna, Z.Pietras, Y.C.Tsai, A.J.Callaghan, H.Hernández, C.V.Robinson, and B.F.Luisi (2010).
The regulatory protein RraA modulates RNA-binding and helicase activities of the E. coli RNA degradosome.
  RNA, 16, 553-562.  
19620987 N.Furnham, J.S.Garavelli, R.Apweiler, and J.M.Thornton (2009).
Missing in action: enzyme functional annotations in biological databases.
  Nat Chem Biol, 5, 521-525.  
19481971 T.R.Ioerger, and J.C.Sacchettini (2009).
Structural genomics approach to drug discovery for Mycobacterium tuberculosis.
  Curr Opin Microbiol, 12, 318-325.  
17668294 E.N.Baker (2007).
Structural genomics as an approach towards understanding the biology of tuberculosis.
  J Struct Funct Genomics, 8, 57-65.  
16672613 H.A.Watkins, and E.N.Baker (2006).
Structural and functional analysis of Rv3214 from Mycobacterium tuberculosis, a protein with conflicting functional annotations, leads to its characterization as a phosphatase.
  J Bacteriol, 188, 3589-3599.
PDB code: 2a6p
16131752 J.M.Johnston, V.L.Arcus, and E.N.Baker (2005).
Structure of naphthoate synthase (MenB) from Mycobacterium tuberculosis in both native and product-bound forms.
  Acta Crystallogr D Biol Crystallogr, 61, 1199-1206.  
16195557 N.Leulliot, S.Quevillon-Cheruel, M.Graille, M.Schiltz, K.Blondeau, J.Janin, and H.Van Tilbeurgh (2005).
Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family.
  Protein Sci, 14, 2751-2758.
PDB code: 2c5q
15036155 A.F.Yakunin, A.A.Yee, A.Savchenko, A.M.Edwards, and C.H.Arrowsmith (2004).
Structural proteomics: a tool for genome annotation.
  Curr Opin Chem Biol, 8, 42-48.  
15502308 P.H.Rehse, C.Kuroishi, and T.H.Tahirov (2004).
Structure of the RNA-processing inhibitor RraA from Thermus thermophilis.
  Acta Crystallogr D Biol Crystallogr, 60, 1997-2002.
PDB code: 1j3l
14675542 C.V.Smith, and J.C.Sacchettini (2003).
Mycobacterium tuberculosis: a model system for structural genomics.
  Curr Opin Struct Biol, 13, 658-664.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.