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PDBsum entry 1vk9

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protein ligands metals links
Unknown function PDB id
1vk9
Jmol
Contents
Protein chain
147 a.a. *
Ligands
UNL
Metals
_ZN ×6
Waters ×9
* Residue conservation analysis
PDB id:
1vk9
Name: Unknown function
Title: Crystal structure of a duf1893 family protein (tm1506) from maritima at 2.70 a resolution
Structure: Conserved hypothetical protein tm1506. Chain: a. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tm1506. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.70Å     R-factor:   0.208     R-free:   0.251
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
Q.Xu et al. (2008). Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution. Proteins, 71, 1546-1552. PubMed id: 18275082 DOI: 10.1002/prot.21992
Date:
06-May-04     Release date:   18-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X1J4  (Q9X1J4_THEMA) -  DUF1893 domain-containing protein
Seq:
Struc:
139 a.a.
147 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     catalytic activity     2 terms  

 

 
DOI no: 10.1002/prot.21992 Proteins 71:1546-1552 (2008)
PubMed id: 18275082  
 
 
Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution.
Q.Xu, P.Kozbial, D.McMullan, S.S.Krishna, S.M.Brittain, S.B.Ficarro, M.DiDonato, M.D.Miller, P.Abdubek, H.L.Axelrod, H.J.Chiu, T.Clayton, L.Duan, M.A.Elsliger, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, H.E.Klock, A.T.Morse, E.Nigoghossian, J.Paulsen, R.Reyes, C.L.Rife, H.van den Bedem, A.White, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of TM1506 from Thermotoga maritima. (A) Stereo ribbon diagram of the TM1506 monomer color-coded from N-terminus (blue) to C-terminus (red). Helices H1-H6 and -strands 1- 5 are indicated. (B) Diagram showing the secondary structural elements of TM1506 superimposed on its primary sequence. The -helices, -strands, and -turns are indicated. The -sheet is indicated by a red A and the -hairpin is depicted as a red loop. Dashed lines indicate regions that are not included in the protein structure.
Figure 2.
Figure 2. ADP-ribosylation reaction, model of TM1506 with conserved residues and ADP-ribose shown on its surface, and sequence alignment. (A) Proposed reaction from NAD^+ to ADP-ribosylated Asp56. (B) Residues conserved in TM1506 are shown on its surface, where the intensity of red color indicates the degree of conservation. The ADP-ribose (shown as a stick model colored by atom type: carbon, green; nitrogen, blue; oxygen, red; phosphorus, orange) was manually fitted into the extra electron density in the active site; metals and waters are shown as spheres (zinc, blue; magnesium, green; water, red). (C) Multiple sequence alignment of TM1506 and its homologs. The intensity of red color indicates the degree of sequence conservation. The conservation scores (0, not conserved; 4, highly conserved) were derived from an analysis using rate4site software using all available homologs of TM1506 and not just those shown in the alignment. The positions of the most conserved residues in TM1506 are indicated above the alignment. Homologs of TM1506 used in the alignment include: ZP_01189901, conserved hypothetical protein from Halothermothrix orenii H 168; YP_001244876, hypothetical protein Tpet_1286 from Thermotoga petrophila RKU-1; ZP_01354436, putative TonB-dependent outer membrane receptor from Clostridium phytofermentans ISDg; YP_001319085, domain of unknown function DUF1893 from Alkaliphilus metalliredigenes QYMF; YP_101571, putative TonB-dependent outer membrane receptor from Bacteroides fragilis YCH46; NP_809874, hypothetical protein BT0961 from Bacteroides thetaiotaomicron VPI-5482. (D) The site of ADP-ribosylation. A plausible model of ADP-ribose that fits the density well is shown as a stick model (carbon, grey; nitrogen, blue; oxygen, red; phosphorus, orange); metals and waters are shown as spheres (zinc, blue; magnesium, green; water, red). The experimental map is shown after solvent flattening. Side-chain atoms of Asp56 and Cys113 are shown as sticks (carbon, yellow; oxygen, red).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 1546-1552) copyright 2008.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20133595 R.Gonzalez, L.L.Jennings, M.Knuth, A.P.Orth, H.E.Klock, W.Ou, J.Feuerhelm, M.V.Hull, E.Koesema, Y.Wang, J.Zhang, C.Wu, C.Y.Cho, A.I.Su, S.Batalov, H.Chen, K.Johnson, B.Laffitte, D.G.Nguyen, E.Y.Snyder, P.G.Schultz, J.L.Harris, and S.A.Lesley (2010).
Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency.
  Proc Natl Acad Sci U S A, 107, 3552-3557.  
18931379 F.Kiefer, K.Arnold, M.Künzli, L.Bordoli, and T.Schwede (2009).
The SWISS-MODEL Repository and associated resources.
  Nucleic Acids Res, 37, D387-D392.  
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