PDBsum entry 1vhv

Transferase

PDB id

1vhv

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Contents

			Protein chains

					251 a.a. *

			Waters ×363

* Residue conservation analysis

PDB id:

1vhv

Links

Name:

Transferase

Title:

Crystal structure of diphthine synthase

Structure:

Diphthine synthase. Chain: a, b. Synonym: diphthamide biosynthesis methyltransferase. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Gene: dphb, af0381. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.75Å

R-factor:

0.211

R-free:

0.254

Authors:

Structural Genomix

Key ref:

J.Badger et al. (2005). Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins, 60, 787-796. PubMed id: 16021622 DOI: 10.1002/prot.20541

Date:

01-Dec-03

Release date:

30-Dec-03

PROCHECK

	Headers

	References

Protein chains

O29866 (DPHB_ARCFU) - Diphthine synthase from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: Struc:					251 a.a. 251 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.2.1.1.98 - diphthine synthase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

2-[(3S)-amino-3-carboxypropyl]-L-histidyl-[translation elongation factor 2] + 3 S-adenosyl-L-methionine = diphthine-[translation elongation factor 2] + 3 S-adenosyl-L-homocysteine + 3 H⁺

2-[(3S)-amino-3-carboxypropyl]-L-histidyl-[translation elongation factor 2]	+	3 × S-adenosyl-L-methionine	=	diphthine-[translation elongation factor 2]	+	3 × S-adenosyl-L-homocysteine	+	3 × H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/prot.20541	Proteins 60:787-796 (2005)
PubMed id: 16021622

Structural analysis of a set of proteins resulting from a bacterial genomics project.

J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, T.J.Harris.

ABSTRACT

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

Selected figure(s)



	Figure 1. Figure 1. Ribbon diagrams[54] of the eleven structures described in the Results and Discussion section: (A) monomer from the dapE structure (1VGY), (B) homodimer from the nudE structure (1VHG), (C) monomer from the DUS structure (1VHN), (D) monomer from the ysdC structure, 1VHE, (E) monomer from the frwX structure, 1VHO, (F) monomer from the perB structure (1VIZ), (G) monomer from the plsX structure (1VI1), (H) monomer from the yqgF structure (1VHX), (I) monomer from the yigZ structure (1VI7), (J) monomer from the YiiM structure (1O65), (K) the novel sufD structure (1VH4) with the homodimer interface in the center.

Literature references that cite this PDB file's key reference

PubMed id

Reference

22505259

A.T.Brunger, D.Das, A.M.Deacon, J.Grant, T.C.Terwilliger, R.J.Read, P.D.Adams, M.Levitt, and G.F.Schröder (2012).
Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

Acta Crystallogr D Biol Crystallogr, 68, 391-403.

PDB code:

3tx8

21543842

C.Björkelid, T.Bergfors, L.M.Henriksson, A.L.Stern, T.Unge, S.L.Mowbray, and T.A.Jones (2011).
Structural and functional studies of mycobacterial IspD enzymes.

Acta Crystallogr D Biol Crystallogr, 67, 403-414.

PDB codes:

2xwl 2xwm 2xwn

19691449

A.Fatehullah, C.Doherty, G.Pivato, G.Allen, L.Devine, J.Nelson, and D.J.Timson (2010).
Interactions of the 67 kDa laminin receptor and its precursor with laminin.

Biosci Rep, 30, 73-79.

20032312

A.V.Kajava, U.Baxa, and A.C.Steven (2010).
Beta arcades: recurring motifs in naturally occurring and disease-related amyloid fibrils.

FASEB J, 24, 1311-1319.

20138056

B.P.Nocek, D.M.Gillner, Y.Fan, R.C.Holz, and A.Joachimiak (2010).
Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.

J Mol Biol, 397, 617-626.

PDB codes:

3ic1 3isz

20305088

E.Karaca, A.S.Melquiond, S.J.de Vries, P.L.Kastritis, and A.M.Bonvin (2010).
Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.

Mol Cell Proteomics, 9, 1784-1794.

20877901

L.Cipolla, L.Gabrielli, D.Bini, L.Russo, and N.Shaikh (2010).
Kdo: a critical monosaccharide for bacteria viability.

Nat Prod Rep, 27, 1618-1629.

19917666

N.Kurochkina, T.Yardeni, and M.Huizing (2010).
Molecular modeling of the bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase and predictions of structural effects of mutations associated with HIBM and sialuria.

Glycobiology, 20, 322-337.

18712420

D.M.Gillner, D.L.Bienvenue, B.P.Nocek, A.Joachimiak, V.Zachary, B.Bennett, and R.C.Holz (2009).
The dapE-encoded N-succinyl-L: ,L: -diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues.

J Biol Inorg Chem, 14, 1.

19361433

K.Wada, N.Sumi, R.Nagai, K.Iwasaki, T.Sato, K.Suzuki, Y.Hasegawa, S.Kitaoka, Y.Minami, F.W.Outten, Y.Takahashi, and K.Fukuyama (2009).
Molecular dynamism of Fe-S cluster biosynthesis implicated by the structure of the SufC(2)-SufD(2) complex.

J Mol Biol, 387, 245-258.

PDB code:

2zu0

19074383

S.Baur, J.Marles-Wright, S.Buckenmaier, R.J.Lewis, and W.Vollmer (2009).
Synthesis of CDP-activated ribitol for teichoic acid precursors in Streptococcus pneumoniae.

J Bacteriol, 191, 1200-1210.

PDB codes:

2vsh 2vsi

18338382

A.Angelini, L.Cendron, S.Goncalves, G.Zanotti, and L.Terradot (2008).
Structural and enzymatic characterization of HP0496, a YbgC thioesterase from Helicobacter pylori.

Proteins, 72, 1212-1221.

PDB code:

2pzh

18413861

A.Petrovic, C.T.Davis, K.Rangachari, B.Clough, R.J.Wilson, and J.F.Eccleston (2008).
Hydrodynamic characterization of the SufBC and SufCD complexes and their interaction with fluorescent adenosine nucleotides.

Protein Sci, 17, 1264-1274.

18322036

C.Ayala-Castro, A.Saini, and F.W.Outten (2008).
Fe-S cluster assembly pathways in bacteria.

Microbiol Mol Biol Rev, 72, 110.

18755835

E.Purta, K.H.Kaminska, J.M.Kasprzak, J.M.Bujnicki, and S.Douthwaite (2008).
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.

RNA, 14, 2234-2244.

18227433

F.R.Salsbury, S.T.Knutson, L.B.Poole, and J.S.Fetrow (2008).
Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid.

Protein Sci, 17, 299-312.

19018107

H.J.Yoon, M.J.Ku, B.Mikami, and S.W.Suh (2008).
Structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Haemophilus influenzae complexed with the substrate 3-deoxy-manno-octulosonate in the beta-configuration.

Acta Crystallogr D Biol Crystallogr, 64, 1292-1294.

PDB code:

3duv

18063583

K.V.Jamieson, J.Wu, S.R.Hubbard, and D.Meruelo (2008).
Crystal structure of the human laminin receptor precursor.

J Biol Chem, 283, 3002-3005.

PDB code:

3bch

18188181

L.M.Velloso, S.S.Bhaskaran, R.Schuch, V.A.Fischetti, and C.E.Stebbins (2008).
A structural basis for the allosteric regulation of non-hydrolysing UDP-GlcNAc 2-epimerases.

EMBO Rep, 9, 199-205.

PDB code:

3beo

18596200

M.W.Vetting, D.C.Bareich, M.Yu, and J.S.Blanchard (2008).
Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N(alpha)-acetylation of ribosomal protein S18.

Protein Sci, 17, 1781-1790.

PDB codes:

2cnm 2cns 2cnt

18491919

P.Smith, P.H.Szu, C.Bui, H.W.Liu, and S.C.Tsai (2008).
Structure and mutagenic conversion of E1 dehydrase: at the crossroads of dehydration, amino transfer, and epimerization.

Biochemistry, 47, 6329-6341.

18461181

R.M.Ward, S.Erdin, T.A.Tran, D.M.Kristensen, A.M.Lisewski, and O.Lichtarge (2008).
De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features.

PLoS ONE, 3, e2136.

18039767

T.Wakamatsu, N.Nakagawa, S.Kuramitsu, and R.Masui (2008).
Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8.

J Bacteriol, 190, 1108-1117.

PDB codes:

2yvm 2yvn 2yvo 2yvp

17675380

D.Leduc, A.Battesti, and E.Bouveret (2007).
The hotdog thioesterase EntH (YbdB) plays a role in vivo in optimal enterobactin biosynthesis by interacting with the ArCP domain of EntB.

J Bacteriol, 189, 7112-7126.

17350958

G.Layer, S.A.Gaddam, C.N.Ayala-Castro, S.Ollagnier-de Choudens, D.Lascoux, M.Fontecave, and F.W.Outten (2007).
SufE transfers sulfur from SufS to SufB for iron-sulfur cluster assembly.

J Biol Chem, 282, 13342-13350.

17872509

G.N.Basturea, and M.P.Deutscher (2007).
Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE.

RNA, 13, 1969-1976.

17189250

H.Matsuoka, K.Hirooka, and Y.Fujita (2007).
Organization and function of the YsiA regulon of Bacillus subtilis involved in fatty acid degradation.

J Biol Chem, 282, 5180-5194.

17873050

J.R.Miller, J.Ohren, R.W.Sarver, W.T.Mueller, P.de Dreu, H.Case, and V.Thanabal (2007).
Phosphopantetheine adenylyltransferase from Escherichia coli: investigation of the kinetic mechanism and role in regulation of coenzyme A biosynthesis.

J Bacteriol, 189, 8196-8205.

17338813

K.L.Tkaczuk, S.Dunin-Horkawicz, E.Purta, and J.M.Bujnicki (2007).
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases.

BMC Bioinformatics, 8, 73.

17919287

Y.Fujita, H.Matsuoka, and K.Hirooka (2007).
Regulation of fatty acid metabolism in bacteria.

Mol Microbiol, 66, 829-839.

17526524

Y.L.Lai, S.C.Yen, S.H.Yu, and J.K.Hwang (2007).
pKNOT: the protein KNOT web server.

Nucleic Acids Res, 35, W420-W424.

17535911

Z.Lin, L.C.Johnson, H.Weissbach, N.Brot, M.O.Lively, and W.T.Lowther (2007).
Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function.

Proc Natl Acad Sci U S A, 104, 9597-9602.

17051231

G.E.Schujman, and D.de Mendoza (2006).
Solving an old puzzle in phospholipid biosynthesis.

Nat Chem Biol, 2, 573-574.

17075135

G.W.Buchko, S.Ni, H.Robinson, E.A.Welsh, H.B.Pakrasi, and M.A.Kennedy (2006).
Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142.

Protein Sci, 15, 2579-2595.

PDB codes:

2f3l 2g0y

16460560

M.von Grotthuss, D.Plewczynski, K.Ginalski, L.Rychlewski, and E.I.Shakhnovich (2006).
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.

BMC Bioinformatics, 7, 53.

16949372

Y.J.Lu, Y.M.Zhang, K.D.Grimes, J.Qi, R.E.Lee, and C.O.Rock (2006).
Acyl-phosphates initiate membrane phospholipid synthesis in Gram-positive pathogens.

Mol Cell, 23, 765-772.

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 code is shown on the right.