PDBsum entry 1vj2

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Metal binding protein PDB id
Protein chains
114 a.a. *
_MN ×2
Waters ×169
* Residue conservation analysis
PDB id:
Name: Metal binding protein
Title: Crystal structure of a novel family of manganese-containing (tm1459) from thermotoga maritima at 1.65 a resolution
Structure: Novel manganese-containing cupin tm1459. Chain: a, b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tm1459. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
1.65Å     R-factor:   0.210     R-free:   0.249
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
L.Jaroszewski et al. (2004). Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution. Proteins, 56, 611-614. PubMed id: 15229893 DOI: 10.1002/prot.20130
03-Dec-03     Release date:   09-Dec-03    
Supersedes: 1o5n
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9X1H0  (Q9X1H0_THEMA) -  Cupin
114 a.a.
114 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     metal ion binding     1 term  


DOI no: 10.1002/prot.20130 Proteins 56:611-614 (2004)
PubMed id: 15229893  
Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution.
L.Jaroszewski, R.Schwarzenbacher, F.von Delft, D.McMullan, L.S.Brinen, J.M.Canaves, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, S.Eshagi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, I.Levin, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, R.Reyes, F.Rezezadeh, 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, K.O.Hodgson, J.Wooley, I.A.Wilson.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. Crystal structure of TM1459 shown as (a) ribbon diagram of Thermotoga maritima TM1459 color coded from N-terminus (blue) to C-terminus (red) showing the domain organization and the location of the manganese ion (purple sphere). The 3[10]-helices (H1, H2), -strands ( [1]- [11] and -sheets A and B are indicated; and (b) ribbon diagram of TM1459 dimer. -strands 1 and 9 of the crossover domain-swap interaction are indicated and are labeled 1 and 9 in the opposing subunit.
Figure 2.
Figure 2. (a) Diagram showing the secondary structure elements in TM1459 superimposed on its primary sequence. -Hairpins are depicted as red loops. Residues coordinating the metal ion are marked with blue dots. (b) The active site of TM1459 showing the proposed manganese ion (Mn), its coordinating residues (His52, His54, His58, His92, and two waters) and Cys106, adjacent to the unidentified density modeled as UNL, is depicted in ball and stick. The atoms are indicated as follows: carbon (grey), oxygen (red), nitrogen (blue), sulfur (orange) and manganese (purple). Metal-ligand bonds are represented as dashed yellow lines.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 611-614) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
16611640 C.R.Simmons, Q.Liu, Q.Huang, Q.Hao, T.P.Begley, P.A.Karplus, and M.H.Stipanuk (2006).
Crystal structure of mammalian cysteine dioxygenase. A novel mononuclear iron center for cysteine thiol oxidation.
  J Biol Chem, 281, 18723-18733.
PDB codes: 2b5h 2gh2
17029242 K.H.Chin, C.C.Chou, A.H.Wang, and S.H.Chou (2006).
Crystal structure of XC5357 from Xanthomonas campestris: a putative tetracenomycin polyketide synthesis protein adopting a novel cupin subfamily structure.
  Proteins, 65, 1046-1050.
PDB code: 2gu9
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.  
16186494 K.McLuskey, S.Cameron, F.Hammerschmidt, and W.N.Hunter (2005).
Structure and reactivity of hydroxypropylphosphonic acid epoxidase in fosfomycin biosynthesis by a cation- and flavin-dependent mechanism.
  Proc Natl Acad Sci U S A, 102, 14221-14226.
PDB codes: 2bnm 2bnn 2bno
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.  
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