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PDBsum entry 1vkb

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protein ligands links
Transferase PDB id
1vkb
Jmol
Contents
Protein chain
148 a.a. *
Ligands
FMT ×3
Waters ×108
* Residue conservation analysis
PDB id:
1vkb
Name: Transferase
Title: Crystal structure of an aig2-like protein (a2ld1, ggact, mgc mus musculus at 1.90 a resolution
Structure: Hypothetical protein. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.90Å     R-factor:   0.136     R-free:   0.171
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
H.E.Klock et al. (2005). Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold. Proteins, 61, 1132-1136. PubMed id: 16224779 DOI: 10.1002/prot.20610
Date:
07-May-04     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q923B0  (A2LD1_MOUSE) -  Gamma-glutamylaminecyclotransferase
Seq:
Struc:
149 a.a.
148 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.2.4  - Gamma-glutamylcyclotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (Gamma-L-glutamyl)-L-amino acid = 5-oxoproline + L-amino acid
(Gamma-L-glutamyl)-L-amino acid
= 5-oxoproline
+
L-amino acid
Bound ligand (Het Group name = FMT)
matches with 50.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular vesicular exosome   1 term 
  Biological process     cellular modified amino acid catabolic process   1 term 
  Biochemical function     transferase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1002/prot.20610 Proteins 61:1132-1136 (2005)
PubMed id: 16224779  
 
 
Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold.
H.E.Klock, R.Schwarzenbacher, Q.Xu, D.McMullan, P.Abdubek, E.Ambing, H.Axelrod, T.Biorac, 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, E.Koesema, A.Kreusch, P.Kuhn, M.D.Miller, K.Moy, E.Nigoghossian, J.Paulsen, K.Quijano, R.Reyes, C.Rife, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, A.White, G.Wolf, 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 13879369 from Mouse. (A) Ribbon diagram color-coded from N-terminus (blue) to C-terminus (red) showing the domain organization. Helices H1-H4 and -strands 1- 7 are indicated. The partial disulfide bond between Cys35 and Cys62 is shown in ball-and-stick. (B) Diagram showing the secondary structure elements in 13879369 superimposed on its primary sequence. The -helices, -strands, -bulges, -turns and disordered regions (dots) are indicated. The -sheet strands are indicated by a red A and B. -Hairpins are depicted as red loops.
Figure 2.
Figure 2. (A) Protein 13879369 in surface representation showing the putative active site cavity with neighboring residues in sticks. Two formic acid and three water molecules located inside the cavity are depicted in sticks and red balls, respectively. (B) Superposition of 13879369 (blue and red) and Ytfp (gray) in ribbon representation. Regions where backbones deviate by RMSD > 4 Å are colored red in 13879369. The two formates shown in red and yellow spheres indicate the position of the putative active site cavity.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 61, 1132-1136) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944236 P.Serrano, B.Pedrini, M.Geralt, K.Jaudzems, B.Mohanty, R.Horst, T.Herrmann, M.A.Elsliger, I.A.Wilson, and K.Wüthrich (2010).
Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1393-1405.
PDB codes: 2ka5 2kl2
17932939 E.Bae, C.A.Bingman, D.J.Aceti, and G.N.Phillips (2008).
Crystal structure of Homo sapiens protein LOC79017.
  Proteins, 70, 588-591.
PDB codes: 2i5t 2q53
17523190 J.M.Aramini, Y.J.Huang, G.V.Swapna, J.R.Cort, P.K.Rajan, R.Xiao, R.Shastry, T.B.Acton, J.Liu, B.Rost, M.A.Kennedy, and G.T.Montelione (2007).
Solution NMR structure of Escherichia coli ytfP expands the structural coverage of the UPF0131 protein domain family.
  Proteins, 68, 789-795.
PDB code: 1xhs
17462573 N.M.Llewellyn, Y.Li, and J.B.Spencer (2007).
Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain.
  Chem Biol, 14, 379-386.  
  16754964 B.L.Lytle, F.C.Peterson, E.M.Tyler, C.L.Newman, D.A.Vinarov, J.L.Markley, and B.F.Volkman (2006).
Solution structure of Arabidopsis thaliana protein At5g39720.1, a member of the AIG2-like protein family.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 490-493.
PDB code: 2g0q
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.