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PDBsum entry 1ct9
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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1ct9

 

 

 

 

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Contents
Protein chains
497 a.a. *
Ligands
IUM ×16
AMP ×4
GLN ×4
Metals
_CL ×4
Waters ×1046
* Residue conservation analysis
PDB id:
1ct9
Name: Ligase
Title: Crystal structure of asparagine synthetase b from escherichia coli
Structure: Asparagine synthetase b. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.197     R-free:   0.297
Authors: T.M.Larsen,S.K.Boehlein,S.M.Schuster,N.G.J.Richards,J.B.Thoden, H.M.Holden,I.Rayment
Key ref:
T.M.Larsen et al. (1999). Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product. Biochemistry, 38, 16146-16157. PubMed id: 10587437 DOI: 10.1021/bi9915768
Date:
20-Aug-99     Release date:   15-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P22106  (ASNB_ECOLI) -  Asparagine synthetase B [glutamine-hydrolyzing] from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		554 a.a.
497 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.6.3.5.4  - asparagine synthase (glutamine-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + L-glutamine + ATP + H2O = L-asparagine + L-glutamate + AMP + diphosphate + H+
L-aspartate
 + L-glutamine
 + ATP
 + H2O
Bound ligand (Het Group name = GLN)
corresponds exactly 		=
L-asparagine
Bound ligand (Het Group name = AMP)
corresponds exactly 		+ L-glutamate
 + AMP
 + diphosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1021/bi9915768 Biochemistry 38:16146-16157 (1999)
PubMed id: 10587437  
 
 
Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.
T.M.Larsen, S.K.Boehlein, S.M.Schuster, N.G.Richards, J.B.Thoden, H.M.Holden, I.Rayment.
 
  ABSTRACT  
 
Asparagine synthetase B catalyzes the assembly of asparagine from aspartate, Mg(2+)ATP, and glutamine. Here, we describe the three-dimensional structure of the enzyme from Escherichia colidetermined and refined to 2.0 A resolution. Protein employed for this study was that of a site-directed mutant protein, Cys1Ala. Large crystals were grown in the presence of both glutamine and AMP. Each subunit of the dimeric protein folds into two distinct domains. The N-terminal region contains two layers of antiparallel beta-sheet with each layer containing six strands. Wedged between these layers of sheet is the active site responsible for the hydrolysis of glutamine. Key side chains employed for positioning the glutamine substrate within the binding pocket include Arg 49, Asn 74, Glu 76, and Asp 98. The C-terminal domain, responsible for the binding of both Mg(2+)ATP and aspartate, is dominated by a five-stranded parallel beta-sheet flanked on either side by alpha-helices. The AMP moiety is anchored to the protein via hydrogen bonds with O(gamma) of Ser 346 and the backbone carbonyl and amide groups of Val 272, Leu 232, and Gly 347. As observed for other amidotransferases, the two active sites are connected by a tunnel lined primarily with backbone atoms and hydrophobic and nonpolar amino acid residues. Strikingly, the three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20571117 B.Sagot, M.Gaysinski, M.Mehiri, J.M.Guigonis, D.Le Rudulier, and G.Alloing (2010).
Osmotically induced synthesis of the dipeptide N-acetylglutaminylglutamine amide is mediated by a new pathway conserved among bacteria.
  Proc Natl Acad Sci U S A, 107, 12652-12657.  
20187643 L.Lund, Y.Fan, Q.Shao, Y.Q.Gao, and F.M.Raushel (2010).
Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation.
  J Am Chem Soc, 132, 3870-3878.  
19371088 M.L.Raber, S.O.Arnett, and C.A.Townsend (2009).
A conserved tyrosyl-glutamyl catalytic dyad in evolutionarily linked enzymes: carbapenam synthetase and beta-lactam synthetase.
  Biochemistry, 48, 4959-4971.  
19270703 N.LaRonde-LeBlanc, M.Resto, and B.Gerratana (2009).
Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.
  Nat Struct Mol Biol, 16, 421-429.
PDB code: 3dla
19726666 S.K.Lim, J.Ju, E.Zazopoulos, H.Jiang, J.W.Seo, Y.Chen, Z.Feng, S.R.Rajski, C.M.Farnet, and B.Shen (2009).
iso-Migrastatin, migrastatin, and dorrigocin production in Streptomyces platensis NRRL 18993 is governed by a single biosynthetic machinery featuring an acyltransferase-less type I polyketide synthase.
  J Biol Chem, 284, 29746-29756.  
20064439 T.A.Knappe, U.Linne, L.Robbel, and M.A.Marahiel (2009).
Insights into the biosynthesis and stability of the lasso peptide capistruin.
  Chem Biol, 16, 1290-1298.  
19569682 Y.Fan, L.Lund, Q.Shao, Y.Q.Gao, and F.M.Raushel (2009).
A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase.
  J Am Chem Soc, 131, 10211-10219.  
17711420 K.Severinov, E.Semenova, A.Kazakov, T.Kazakov, and M.S.Gelfand (2007).
Low-molecular-weight post-translationally modified microcins.
  Mol Microbiol, 65, 1380-1394.  
17656316 S.Duquesne, D.Destoumieux-Garzón, S.Zirah, C.Goulard, J.Peduzzi, and S.Rebuffat (2007).
Two enzymes catalyze the maturation of a lasso peptide in Escherichia coli.
  Chem Biol, 14, 793-803.  
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
16809541 A.Nakamura, M.Yao, S.Chimnaronk, N.Sakai, and I.Tanaka (2006).
Ammonia channel couples glutaminase with transamidase reactions in GatCAB.
  Science, 312, 1954-1958.
PDB codes: 2df4 2dqn 2f2a 2g5h 2g5i
16377694 H.Ren, and J.Liu (2006).
AsnB is involved in natural resistance of Mycobacterium smegmatis to multiple drugs.
  Antimicrob Agents Chemother, 50, 250-255.  
17185229 J.A.Gutierrez, Y.X.Pan, L.Koroniak, J.Hiratake, M.S.Kilberg, and N.G.Richards (2006).
An inhibitor of human asparagine synthetase suppresses proliferation of an L-asparaginase-resistant leukemia cell line.
  Chem Biol, 13, 1339-1347.  
16387658 J.D.Mougous, D.H.Lee, S.C.Hubbard, M.W.Schelle, D.J.Vocadlo, J.M.Berger, and C.R.Bertozzi (2006).
Molecular basis for G protein control of the prokaryotic ATP sulfurylase.
  Mol Cell, 21, 109-122.
PDB code: 1zun
16756505 N.G.Richards, and M.S.Kilberg (2006).
Asparagine synthetase chemotherapy.
  Annu Rev Biochem, 75, 629-654.  
16425030 R.A.Cañas, F.de la Torre, F.M.Cánovas, and F.R.Cantón (2006).
High levels of asparagine synthetase in hypocotyls of pine seedlings suggest a role of the enzyme in re-allocation of seed-stored nitrogen.
  Planta, 224, 83-95.  
16597959 W.Zhang, B.D.Ames, S.C.Tsai, and Y.Tang (2006).
Engineered biosynthesis of a novel amidated polyketide, using the malonamyl-specific initiation module from the oxytetracycline polyketide synthase.
  Appl Environ Microbiol, 72, 2573-2580.  
15987679 F.Levitin, O.Stern, M.Weiss, C.Gil-Henn, R.Ziv, Z.Prokocimer, N.I.Smorodinsky, D.B.Rubinstein, and D.H.Wreschner (2005).
The MUC1 SEA module is a self-cleaving domain.
  J Biol Chem, 280, 33374-33386.  
16113715 N.J.Kershaw, M.E.Caines, M.C.Sleeman, and C.J.Schofield (2005).
The enzymology of clavam and carbapenem biosynthesis.
  Chem Commun (Camb), (), 4251-4263.  
15805504 Y.Mitani, X.Meng, Y.Kamagata, and T.Tamura (2005).
Characterization of LtsA from Rhodococcus erythropolis, an enzyme with glutamine amidotransferase activity.
  J Bacteriol, 187, 2582-2591.  
15466049 E.L.Hendrickson, R.Kaul, Y.Zhou, D.Bovee, P.Chapman, J.Chung, E.Conway de Macario, J.A.Dodsworth, W.Gillett, D.E.Graham, M.Hackett, A.K.Haydock, A.Kang, M.L.Land, R.Levy, T.J.Lie, T.A.Major, B.C.Moore, I.Porat, A.Palmeiri, G.Rouse, C.Saenphimmachak, D.Söll, S.Van Dien, T.Wang, W.B.Whitman, Q.Xia, Y.Zhang, F.W.Larimer, M.V.Olson, and J.A.Leigh (2004).
Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis.
  J Bacteriol, 186, 6956-6969.  
15511226 F.A.Lunn, and S.L.Bearne (2004).
Alternative substrates for wild-type and L109A E. coli CTP synthases: kinetic evidence for a constricted ammonia tunnel.
  Eur J Biochem, 271, 4204-4212.  
15150276 H.H.Lin, G.W.Chang, J.Q.Davies, M.Stacey, J.Harris, and S.Gordon (2004).
Autocatalytic cleavage of the EMR2 receptor occurs at a conserved G protein-coupled receptor proteolytic site motif.
  J Biol Chem, 279, 31823-31832.  
15189875 J.D.Lawson, E.Pate, I.Rayment, and R.G.Yount (2004).
Molecular dynamics analysis of structural factors influencing back door pi release in myosin.
  Biophys J, 86, 3794-3803.  
15498940 V.M.Coiro, A.Di Nola, M.A.Vanoni, M.Aschi, A.Coda, B.Curti, and D.Roccatano (2004).
Molecular dynamics simulation of the interaction between the complex iron-sulfur flavoprotein glutamate synthase and its substrates.
  Protein Sci, 13, 2979-2991.  
12764229 B.A.Manjasetty, J.Powlowski, and A.Vrielink (2003).
Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate.
  Proc Natl Acad Sci U S A, 100, 6992-6997.
PDB code: 1nvm
14506286 D.E.Pilloff, and T.S.Leyh (2003).
Allosteric and catalytic functions of the PPi-binding motif in the ATP sulfurylase-GTPase system.
  J Biol Chem, 278, 50435-50441.  
12684518 M.Goto, R.Omi, I.Miyahara, M.Sugahara, and K.Hirotsu (2003).
Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction.
  J Biol Chem, 278, 22964-22971.
PDB codes: 1j1z 1j20 1j21 1kh3
12890666 M.T.Miller, B.Gerratana, A.Stapon, C.A.Townsend, and A.C.Rosenzweig (2003).
Crystal structure of carbapenam synthetase (CarA).
  J Biol Chem, 278, 40996-41002.
PDB codes: 1q15 1q19
12799468 R.Amaro, E.Tajkhorshid, and Z.Luthey-Schulten (2003).
Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF.
  Proc Natl Acad Sci U S A, 100, 7599-7604.  
11839304 A.Douangamath, M.Walker, S.Beismann-Driemeyer, M.C.Vega-Fernandez, R.Sterner, and M.Wilmanns (2002).
Structural evidence for ammonia tunneling across the (beta alpha)(8) barrel of the imidazole glycerol phosphate synthase bienzyme complex.
  Structure, 10, 185-193.
PDB codes: 1gpw 1k9v
12372836 A.Magalon, C.Frixon, J.Pommier, G.Giordano, and F.Blasco (2002).
In vivo interactions between gene products involved in the final stages of molybdenum cofactor biosynthesis in Escherichia coli.
  J Biol Chem, 277, 48199-48204.  
11880622 B.Min, J.T.Pelaschier, D.E.Graham, D.Tumbula-Hansen, and D.Söll (2002).
Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation.
  Proc Natl Acad Sci U S A, 99, 2678-2683.  
12413541 C.A.Townsend (2002).
New reactions in clavulanic acid biosynthesis.
  Curr Opin Chem Biol, 6, 583-589.  
11809762 C.T.Lemke, and P.L.Howell (2002).
Substrate induced conformational changes in argininosuccinate synthetase.
  J Biol Chem, 277, 13074-13081.
PDB codes: 1kp2 1kp3
12130656 J.B.Thoden, X.Huang, F.M.Raushel, and H.M.Holden (2002).
Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia.
  J Biol Chem, 277, 39722-39727.
PDB code: 1m6v
11842094 K.O.Broschat, C.Gorka, J.D.Page, C.L.Martin-Berger, M.S.Davies, H.C.Huang Hc, E.A.Gulve, W.J.Salsgiver, and T.P.Kasten (2002).
Kinetic characterization of human glutamine-fructose-6-phosphate amidotransferase I: potent feedback inhibition by glucosamine 6-phosphate.
  J Biol Chem, 277, 14764-14770.  
11844799 M.Goto, Y.Nakajima, and K.Hirotsu (2002).
Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action.
  J Biol Chem, 277, 15890-15896.
PDB codes: 1kh1 1kh2 1kor
12409610 M.T.Miller, B.O.Bachmann, C.A.Townsend, and A.C.Rosenzweig (2002).
The catalytic cycle of beta -lactam synthetase observed by x-ray crystallographic snapshots.
  Proc Natl Acad Sci U S A, 99, 14752-14757.
PDB codes: 1m1z 1mb9 1mbz 1mc1
11967268 R.H.van den Heuvel, D.Ferrari, R.T.Bossi, S.Ravasio, B.Curti, M.A.Vanoni, F.J.Florencio, and A.Mattevi (2002).
Structural studies on the synchronization of catalytic centers in glutamate synthase.
  J Biol Chem, 277, 24579-24583.
PDB codes: 1llw 1llz 1lm1
11395405 X.Huang, H.M.Holden, and F.M.Raushel (2001).
Channeling of substrates and intermediates in enzyme-catalyzed reactions.
  Annu Rev Biochem, 70, 149-180.  
10809725 A.F.Kisselev, Z.Songyang, and A.L.Goldberg (2000).
Why does threonine, and not serine, function as the active site nucleophile in proteasomes?
  J Biol Chem, 275, 14831-14837.  
10850988 A.K.Bera, S.Chen, J.L.Smith, and H.Zalkin (2000).
Temperature-dependent function of the glutamine phosphoribosylpyrophosphate amidotransferase ammonia channel and coupling with glycinamide ribonucleotide synthetase in a hyperthermophile.
  J Bacteriol, 182, 3734-3739.  
10985764 B.O.Bachmann, and C.A.Townsend (2000).
Kinetic mechanism of the beta-lactam synthetase of Streptomyces clavuligerus.
  Biochemistry, 39, 11187-11193.  
11188694 C.Binda, R.T.Bossi, S.Wakatsuki, S.Arzt, A.Coda, B.Curti, M.A.Vanoni, and A.Mattevi (2000).
Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase.
  Structure, 8, 1299-1308.
PDB code: 1ea0
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.

 

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