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PDBsum entry 1vkm

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protein ligands metals Protein-protein interface(s) links
Biosynthetic protein PDB id
1vkm
Jmol
Contents
Protein chains
(+ 0 more) 292 a.a. *
Ligands
UNL ×6
EDO ×11
Metals
_MN ×16
Waters ×987
* Residue conservation analysis
PDB id:
1vkm
Name: Biosynthetic protein
Title: Crystal structure of an indigoidine synthase a (idga)-like p (tm1464) from thermotoga maritima msb8 at 1.90 a resolution
Structure: Conserved hypothetical protein tm1464. Chain: a, b, c, d, e, f. Engineered: yes. Other_details: possibly involved in carbohydrate metabolism
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm1464. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Hexamer (from PQS)
Resolution:
1.90Å     R-factor:   0.156     R-free:   0.200
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
I.Levin et al. (2005). Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold. Proteins, 59, 864-868. PubMed id: 15822122 DOI: 10.1002/prot.20420
Date:
09-Jun-04     Release date:   29-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X1H5  (PSUG_THEMA) -  Pseudouridine-5'-phosphate glycosidase
Seq:
Struc:
285 a.a.
292 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1002/prot.20420 Proteins 59:864-868 (2005)
PubMed id: 15822122  
 
 
Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.
I.Levin, M.D.Miller, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, T.Biorac, J.Cambell, J.M.Canaves, H.J.Chiu, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, M.Hornsby, L.Jaroszewski, C.Karlak, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, R.Page, K.Quijano, R.Reyes, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of TM1464. (A) Stereo ribbon diagram of T. maritima TM1464 color-coded from N-terminus (blue) to C-terminus (red), showing the domain organization. Helices H1-H12, and -strands ( 1- 11) are indicated. (B) Diagram showing the secondary structure elements in TM1464 superimposed on its primary sequence. The -helices, 3[10]-helices, -bulges, and -turns are indicated. The -sheet strands are indicated by a red A, and -hairpins are depicted as red loops.
Figure 2.
Figure 2. (A) The TM1464 trimer viewed along the 3-fold axis. One subunit is shown in blue. The 3 UNLs bound to the putative active sites are shown as red spheres. (B) TM1464 shown in surface representation illustrating the narrow active site pocket, with the bound UNL in ball-and-stick configuration. (C) Close-up of the putative active site. TM1464 is shown in ribbon representation with the UNL, manganese, and interacting residues and waters in ball-and-stick configuration (see text). A SigmaA-weighted Fo-Fc omit map contoured at 3.0 is shown for the UNL, manganese, and coordinating waters. Putative H-bond interactions between the UNL and the protein are shown in yellow dotted lines.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 59, 864-868) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21445639 E.S.Julfayev, R.J.McLaughlin, Y.P.Tao, and W.A.McLaughlin (2011).
A new approach to assess and predict the functional roles of proteins across all known structures.
  J Struct Funct Genomics, 12, 9.  
18591240 A.Preumont, K.Snoussi, V.Stroobant, J.F.Collet, and E.Van Schaftingen (2008).
Molecular identification of pseudouridine-metabolizing enzymes.
  J Biol Chem, 283, 25238-25246.  
18940666 T.Oja, K.Palmu, H.Lehmussola, O.Leppäranta, K.Hännikäinen, J.Niemi, P.Mäntsälä, and M.Metsä-Ketelä (2008).
Characterization of the alnumycin gene cluster reveals unusual gene products for pyran ring formation and dioxan biosynthesis.
  Chem Biol, 15, 1046-1057.  
17237222 H.Takahashi, T.Kumagai, K.Kitani, M.Mori, Y.Matoba, and M.Sugiyama (2007).
Cloning and characterization of a Streptomyces single module type non-ribosomal peptide synthetase catalyzing a blue pigment synthesis.
  J Biol Chem, 282, 9073-9081.  
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
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