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Structure paper

タイトルCombining functional and structural genomics to sample the essential Burkholderia structome.
ジャーナル・号・ページPlos One, Vol. 8, Page e53851-e53851, Year 2013
掲載日2008年5月18日 (構造データの登録日)
著者Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. ...Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
リンクPlos One / PubMed:23382856
手法X線回折
解像度1.35 - 2.65 Å
構造データ

PDB-3d63:
Crystal structure of inorganic pyrophosphatase from Burkholderia pseudomallei
手法: X-RAY DIFFRACTION / 解像度: 2.3 Å

PDB-3dah:
2.3 A crystal structure of ribose-phosphate pyrophosphokinase from Burkholderia pseudomallei
手法: X-RAY DIFFRACTION / 解像度: 2.3 Å

PDB-3eiz:
Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei, H32 crystal form
手法: X-RAY DIFFRACTION / 解像度: 1.88 Å

PDB-3ej2:
Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei with bound 5-amino-1-(4-chlorophenyl)-1h-pyrazole-4-carbonitrile, H32 crystal form
手法: X-RAY DIFFRACTION / 解像度: 2.12 Å

PDB-3ek2:
Crystal structure of eonyl-(acyl carrier protein) reductase from burkholderia pseudomallei 1719b
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-3ezo:
Crystal structure of acyl-carrier-protein s-malonyltransferase from burkholderia pseudomallei 1710b
手法: X-RAY DIFFRACTION / 解像度: 2.05 Å

PDB-3f0f:
Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with hydrolyzed CDP
手法: X-RAY DIFFRACTION / 解像度: 2.09 Å

PDB-3ftp:
Crystal structure of 3-Ketoacyl-(acyl-carrier-protein) reductase from Burkholderia pseudomallei at 2.05 A resolution
手法: X-RAY DIFFRACTION / 解像度: 2.05 Å

PDB-3gk0:
Crystal structure of pyridoxal phosphate biosynthetic protein from Burkholderia pseudomallei
手法: X-RAY DIFFRACTION / 解像度: 2.28 Å

PDB-3gk3:
Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-3gvf:
1.7 Angstrom crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei bound with phosphate
手法: X-RAY DIFFRACTION / 解像度: 1.75 Å

PDB-3gwa:
1.6 Angstrom crystal structure of 3-oxoacyl-(acyl-carrier-protein) synthase III
手法: X-RAY DIFFRACTION / 解像度: 1.6 Å

PDB-3gwe:
2.1 Angstrom crystal structure of 3-oxoacyl-(acyl-carrier-protein) synthase III
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-3iml:
Crystal Structure Of S-Adenosylmethionine Synthetase From Burkholderia Pseudomallei
手法: X-RAY DIFFRACTION / 解像度: 2.35 Å

PDB-3sz8:
Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei
手法: X-RAY DIFFRACTION / 解像度: 2.05 Å

PDB-3t4c:
Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia ambifaria
手法: X-RAY DIFFRACTION / 解像度: 1.95 Å

PDB-3tml:
Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-3tmq:
Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei in complex with D-arabinose-5-phosphate
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-3txy:
Structure of an Isochorismatase family protein (BTH_II2229) from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-3u7j:
Crystal structure of Ribose-5-phosphate isomerase A from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-3ue9:
Crystal structure of Adenylosuccinate synthetase (AMPSase) (purA) from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.95 Å

PDB-3uk1:
Crystal structure of a transketolase from Burkholderia thailandensis with an oxidized cysteinesulfonic acid in the active site
手法: X-RAY DIFFRACTION / 解像度: 2.15 Å

PDB-3uk2:
The structure of Pantothenate synthetase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.25 Å

PDB-3und:
Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-3upt:
Crystal structure of a transketolase from Burkholderia pseudomallei bound to TPP, calcium and ribose-5-phosphate
手法: X-RAY DIFFRACTION / 解像度: 2.4 Å

PDB-3urr:
Structure of PTS IIA-like nitrogen-regulatory protein PtsN (BTH_I0484) (ptsN)
手法: X-RAY DIFFRACTION / 解像度: 1.397 Å

PDB-3uw1:
Crystal structure of ribose-5-phosphate isomerase a from burkholderia thailandensis with ribose-5-phosphate
手法: X-RAY DIFFRACTION / 解像度: 1.71 Å

PDB-3uw2:
X-ray Crystal Structure of Phosphoglucomutase/phosphomannomutase family protein (BTH_I1489)from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.95 Å

PDB-3uw3:
Crystal Structure of an Aspartate-Semialdehyde Dehydrogenase from Burkholderia Thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.55 Å

PDB-3v2i:
Structure of a Peptidyl-tRNA hydrolase (PTH) from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.65 Å

PDB-3v7n:
Crystal structure of Threonine synthase (thrC) from from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.4 Å

PDB-3v8h:
Crystal structure of Thymidylate Synthase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.65 Å

PDB-3v9o:
Crystal structure of Dihydroneopterin aldolase (BTH_I0291) from Burkholderia thailendensis bound to guanine.
手法: X-RAY DIFFRACTION / 解像度: 1.451 Å

PDB-3v9p:
Crystal structure of Thymidylate kinase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-3vav:
Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4ddo:
Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase ii from burkholderia vietnamiensis
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-4dfe:
Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans
手法: X-RAY DIFFRACTION / 解像度: 2.35 Å

PDB-4dhe:
Crystal structure of a probable GTP-binding protein engB from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.2 Å

PDB-4dhk:
Crystal structure of a deoxycytidine triphosphate deaminase (dCTP deaminase) from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.05 Å

PDB-4dut:
The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.5 Å

PDB-4dz4:
X-ray crystal structure of a hypothetical Agmatinase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.7 Å

PDB-4e4t:
Crystal structure of Phosphoribosylaminoimidazole carboxylase, ATPase subunit from Burkholderia ambifaria
手法: X-RAY DIFFRACTION / 解像度: 1.55 Å

PDB-4efi:
Crystal Structure of 3-oxoacyl-(Acyl-carrier protein) Synthase from Burkholderia Xenovorans LB400
手法: X-RAY DIFFRACTION / 解像度: 1.35 Å

PDB-4eg0:
Crystal Structure of D-alanine--D-alanine ligase from Burkholderia ambifaria
手法: X-RAY DIFFRACTION / 解像度: 1.65 Å

PDB-4egj:
Crystal structure of D-alanine-D-alanine ligase from Burkholderia xenovorans
手法: X-RAY DIFFRACTION / 解像度: 2.3 Å

PDB-4ek2:
The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate
手法: X-RAY DIFFRACTION / 解像度: 2 Å

PDB-4eqy:
Crystal structure of Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4ewg:
Crystal structure of a Beta-ketoacyl synthase from Burkholderia phymatum STM815
手法: X-RAY DIFFRACTION / 解像度: 2.25 Å

PDB-4exq:
CRYSTAL STRUCTURE of UROPORPHYRINOGEN DECARBOXYLASE (UPD) FROM BURKHOLDERIA THAILANDENSIS E264
手法: X-RAY DIFFRACTION / 解像度: 1.65 Å

PDB-4f2g:
The Crystal Structure of Ornithine carbamoyltransferase from Burkholderia thailandensis E264
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-4f32:
Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase II from Burkholderia vietnamiensis in complex with platencin
手法: X-RAY DIFFRACTION / 解像度: 1.9 Å

PDB-4f3n:
High resolution native crystal structure of an uncharacterized ACR, COG1565 superfamily protein from Burkholderia thailandensis, solved by iodide ion SAD
手法: X-RAY DIFFRACTION / 解像度: 1.75 Å

PDB-4f3y:
X-Ray Crystal Structure of Dihydrodipicolinate reductase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-4f4h:
Crystal structure of a Glutamine dependent NAD+ synthetase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 1.75 Å

PDB-4f7d:
Crystal structure of ferredoxin-NADP reductase from burkholderia thailandensis E264
手法: X-RAY DIFFRACTION / 解像度: 2.35 Å

PDB-4fk8:
Crystal structure of FERREDOXIN-NADP REDUCTASE from burkholderia thailandensis E264 with bound FAD
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-4fry:
The structure of a putative signal-transduction protein with CBS domains from Burkholderia ambifaria MC40-6
手法: X-RAY DIFFRACTION / 解像度: 2.1 Å

PDB-4g1k:
Crystal structure of triosephosphate isomerase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.35 Å

PDB-4g67:
Crystal structure of a COG1565 superfamily member and likely methyl transferase from Burkholderia thailandensis bound to S-adenosyl-homocysteine
手法: X-RAY DIFFRACTION / 解像度: 1.8 Å

PDB-4ghk:
X-ray Crystal Structure of Gamma-glutamyl phosphate reductase from Burkholderia thailandensis
手法: X-RAY DIFFRACTION / 解像度: 2.25 Å

PDB-4h3y:
Crystal structure of an asymmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in one half-site
手法: X-RAY DIFFRACTION / 解像度: 2.5 Å

PDB-4h3z:
Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in both half-sites
手法: X-RAY DIFFRACTION / 解像度: 2.15 Å

PDB-4h4g:
Crystal Structure of (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase from Burkholderia thailandensis E264
手法: X-RAY DIFFRACTION / 解像度: 2.65 Å

化合物

ChemComp-HOH:
WATER

ChemComp-PO4:
PHOSPHATE ION / ホスファ-ト

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP / AMP*YM

ChemComp-928:
5-amino-1-(4-chlorophenyl)-1H-pyrazole-4-carbonitrile / 1-(4-クロロフェニル)-5-アミノ-1H-ピラゾ-ル-4-カルボニトリル

ChemComp-CL:
Unknown entry / クロリド

ChemComp-GOL:
GLYCEROL / グリセロ-ル

ChemComp-MG:
Unknown entry / マグネシウムジカチオン

ChemComp-ZN:
Unknown entry

ChemComp-C5P:
CYTIDINE-5'-MONOPHOSPHATE / CMP

ChemComp-DXP:
1-DEOXY-D-XYLULOSE-5-PHOSPHATE / 1-デオキシ-D-キシルロ-ス5-りん酸

ChemComp-K:
Unknown entry / カリウムカチオン

ChemComp-NA:
Unknown entry / ナトリウムカチオン

ChemComp-PGE:
TRIETHYLENE GLYCOL / トリエチレングリコ-ル

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル

ChemComp-ACT:
ACETATE ION / 酢酸イオン

ChemComp-SO4:
SULFATE ION / 硫酸ジアニオン

ChemComp-A5P:
ARABINOSE-5-PHOSPHATE / D-アラビニト-ル5-りん酸

ChemComp-NO3:
NITRATE ION

ChemComp-EDO:
1,2-ETHANEDIOL / エチレングリコ-ル

ChemComp-CA:
Unknown entry / カルシウムジカチオン

ChemComp-MLT:
D-MALATE / D-りんご酸

ChemComp-PEP:
PHOSPHOENOLPYRUVATE / ホスホエノ-ルピルビン酸

ChemComp-KD0:
3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid / 3-デオキシ-D-manno-2-オクツロソン酸8-りん酸

ChemComp-TPP:
THIAMINE DIPHOSPHATE / 3-[(4-アミノ-2-メチル-5-ピリミジニル)メチル]-4-メチル-5-[2-(ホスホノオキシホスフィナトオキシ)(以下略)

ChemComp-RP5:
5-O-phosphono-beta-D-ribofuranose / β-D-リボフラノ-ス5-りん酸

ChemComp-BR:
BROMIDE ION / ブロミド

ChemComp-R5P:
RIBOSE-5-PHOSPHATE / D-リボ-ス5-りん酸

ChemComp-CIT:
CITRIC ACID / クエン酸


化合物 画像なし

ChemComp-UNL:
Unknown ligand

ChemComp-MLA:
MALONIC ACID / マロン酸

ChemComp-BO3:
BORIC ACID / ほう酸

ChemComp-GUN:
GUANINE / グアニン

ChemComp-MRD:
(4R)-2-METHYLPENTANE-2,4-DIOL / (4R)-2-メチル-2,4-ペンタンジオ-ル / 沈殿剤*YM

ChemComp-MN:
Unknown entry

ChemComp-UNK:
UNKNOWN / (S)-2-アミノ酪酸

ChemComp-FMT:
FORMIC ACID / ギ酸

ChemComp-DMS:
DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド / DMSO, 沈殿剤*YM

ChemComp-D5M:
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / dAMP

ChemComp-IMD:
IMIDAZOLE / 1H-イミダゾ-ル-3-カチオン

ChemComp-N32:
2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid / プラテンシン

ChemComp-UNX:
Unknown entry

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD / FAD*YM

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE / S-アデノシルホモシステイン

由来
  • burkholderia pseudomallei (類鼻疽菌)
  • burkholderia pseudomallei 1710b (類鼻疽菌)
  • burkholderia ambifaria (バクテリア)
  • burkholderia cenocepacia (バクテリア)
  • burkholderia thailandensis (バクテリア)
  • burkholderia thailandensis e264 (バクテリア)
  • burkholderia vietnamiensis (バクテリア)
  • burkholderia xenovorans (バクテリア)
  • burkholderia phymatum (バクテリア)
  • streptomyces platensis (バクテリア)
キーワードHYDROLASE / structural genomics / SSGCID / pyrophosphatase / Seattle Structural Genomics Center for Infectious Disease / TRANSFERASE / BURKHOLDERIA / PSEUDOMALLEI / RIBOSE / PHOSPHATE / PYROPHOSPHOKINASE / Magnesium / Metal binding / Nucleotide biosynthesis / BupsA.00023.a / OXIDOREDUCTASE / enoyl-(acyl carrier protein) reductase / ACYL-CARRIER-PROTEIN S-MALONYLTRANSFERASE / BURKHOLDERIA PSEUDOMALLEI / Acyltransferase / LYASE / NIAID / Isoprene biosynthesis / Metal-binding / 3-KETOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE / deCODE / SBRI / Pyridoxine biosynthesis / acetoacetyl-Co reductase / inorganic pyrophosphatase / acyl carrier protein / synthetase / FabH / S-adenosylmethionine synthetase / ATP-binding / Cobalt / Nucleotide-binding / One-carbon metabolism / Potassium / aldolase barrel / UNKNOWN FUNCTION / Isochorismatase family protein / ISOMERASE / LIGASE / AdSS / BTH_I2245 / IMP-aspartate ligase / thiamine pyrophosphate / ribose-5-phosphate / pentose phosphate pathway / Calvin cycle / AMP / Pantothenate synthetase / TPP / calcium-dependent / co-factor / e pentose phosphate pathway / tkt / Ribose isomerase / Phosphoglucomutase / Phosphorylation / S109 / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / dehydrogenase / RNA / Peptidyl-tRNA hydrolase / Thymidylate synthase / Dihydroneopterin aldolase / Dihydroneopterin / Thymidylate kinase / Burkholderia thailandensis / Burkolderia thailandensis / melioidosis / Ketopantoate hydroxymethyltransferase (KPHMT) / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE II / CELL CYCLE / RAS-like GTPase / cell division / septation / GTP-binding / deaminase / National Institute of Allergy and Infectious Diseases / Agmatinase / purine biosynthesis / ATP binding / ACAIR / CAIR / D-alanine-D-alanine ligase / dAMP / beta helix / BIOSYNTHETIC PROTEIN / NIH / URO-D / HEME BIOSYNTHESIS / carbamoyltransferase / Transferase/Antibiotic / platencin / Transferase-Antibiotic complex / iodide ion phasing / SAD / methyltransferase superfamily / putative uncharacterize protein / similar fold to 1zkd / Dihydrodipicolinate reductase / NAD/NADH / UW / EMERALD BIOSTRUCTURES / FERREDOXIN-NADP REDUCTASE / SIGNALING PROTEIN / CBS domain / Putative signal-transduction protein / TIM barrel / tpiA / D-glyceraldehyde 3-phosphate / glycerone phosphate / gluconeogenesis / glycolysis / S-adenosyl methionine / SAM / AdoMet / SAH / AdoHcy / natural inhibitor / candidate essential gene / Gamma-glutamyl phosphate reductase / trmD / M1G-methyltransferase / G37 methyltransferase / S-adenosyl-methionine / S-adenosyl-homocysteine / tRNA modification / proteobacteria / nitrogen fixation / food pathogen / domain swapped homodimer / tRNA methylation / m1G37 methylation / food parasite / Lipid A biosynthesis / Lipid synthesis / hydrolyase enzyme

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