PDBsum entry 1vk9

Unknown function

PDB id: 1vk9

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 thermotoga 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

Protein chain

Q9X1J4  (Q9X1J4_THEMA) -  DUF1893 domain-containing protein from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 139 a.a.

Struc: 147 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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.