spacer
spacer

PDBsum entry 1o5u

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Unknown function PDB id
1o5u
Jmol
Contents
Protein chains
88 a.a. *
Ligands
UNL ×3
Waters ×282
* Residue conservation analysis
PDB id:
1o5u
Name: Unknown function
Title: Crystal structure of a duf861 family protein (tm1112) from t maritima at 1.83 a resolution
Structure: Novel thermotoga maritima enzyme tm1112. Chain: a, b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tm1112. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.83Å     R-factor:   0.173     R-free:   0.222
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
D.McMullan et al. (2004). Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution. Proteins, 56, 615-618. PubMed id: 15229894 DOI: 10.1002/prot.20139
Date:
06-Oct-03     Release date:   11-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X0J6  (Q9X0J6_THEMA) -  Uncharacterized protein
Seq:
Struc:
89 a.a.
88 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1002/prot.20139 Proteins 56:615-618 (2004)
PubMed id: 15229894  
 
 
Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution.
D.McMullan, R.Schwarzenbacher, L.Jaroszewski, F.von Delft, H.E.Klock, J.Vincent, K.Quijano, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.M.Canaves, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, S.Eshaghi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, C.Karlak, E.Koesema, A.Kreusch, P.Kuhn, I.Levin, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, R.Reyes, F.Rezezadeh, A.Robb, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, S.A.Lesley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of TM1112. A: Ribbon diagram of Thermotoga maritima TM1112 color coded from N-terminus (blue) to C-terminus (red) showing the domain organization viewed along (left) and normal (right) to the barrel axis. Helices (H1, H2), -sheets (A and A ), and -strands ( 1- 7) are indicated. B: Diagram showing the secondary structure elements in TM1112 superimposed on its primary sequence. The -sheets are indicated by a red A or A and the -hairpin is depicted as red loops. Residues adjacent to the the unknown ligand (UNL) molecule are marked with red dots (also see Fig. 2).
Figure 2.
Figure 2. A: The proposed active site of TM1112 is depicted with the unknown ligand molecule (UNL) bound to Lys84 and its coordinating residues (Trp24, Trp33, Glu39, Cys41, Tyr35, and Trp76) in ball and stick. B: Close up view of the active site with a 2Fo-Fc map around Lys84, the covalently-bound UNL and Cys41 contoured at 1 (marine blue). The atoms are indicated as follows: carbon (grey), oxygen (red), nitrogen (blue), sulfur (yellow), and UNL (pink). Potential covalent bonds for the UNL ligand are represented as dashed pink lines, but until ligand identification, these are quite speculative.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 615-618) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944235 B.Mohanty, P.Serrano, B.Pedrini, K.Jaudzems, M.Geralt, R.Horst, T.Herrmann, M.A.Elsliger, I.A.Wilson, and K.Wüthrich (2010).
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1381-1392.
PDB codes: 2k9z 2ka0
19478949 G.Agarwal, M.Rajavel, B.Gopal, and N.Srinivasan (2009).
Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold.
  PLoS One, 4, e5736.  
16783794 Q.Xu, R.Schwarzenbacher, S.S.Krishna, D.McMullan, S.Agarwalla, K.Quijano, P.Abdubek, E.Ambing, H.Axelrod, T.Biorac, J.M.Canaves, H.J.Chiu, M.A.Elsliger, C.Grittini, S.K.Grzechnik, M.DiDonato, J.Hale, E.Hampton, G.W.Han, J.Haugen, M.Hornsby, L.Jaroszewski, H.E.Klock, M.W.Knuth, E.Koesema, A.Kreusch, P.Kuhn, M.D.Miller, K.Moy, E.Nigoghossian, J.Paulsen, R.Reyes, C.Rife, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, A.White, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2006).
Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution.
  Proteins, 64, 808-813.
PDB code: 1vr3
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.  
16211521 R.Page, A.M.Deacon, S.A.Lesley, and R.C.Stevens (2005).
Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins.
  J Struct Funct Genomics, 6, 209-217.  
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 codes are shown on the right.