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PDBsum entry 2awo

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protein ligands metals Protein-protein interface(s) links
Transport protein PDB id
2awo
Jmol
Contents
Protein chains
372 a.a. *
299 a.a. *
Ligands
ADP ×4
Metals
_MG ×4
* Residue conservation analysis
PDB id:
2awo
Name: Transport protein
Title: Crystal structure of the adp-mg-bound e. Coli malk (crystall adp-mg)
Structure: Maltose/maltodextrin import atp-binding protein m chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: malk. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.239     R-free:   0.277
Authors: G.Lu,J.M.Westbrooks,A.L.Davidson,J.Chen
Key ref:
G.Lu et al. (2005). ATP hydrolysis is required to reset the ATP-binding cassette dimer into the resting-state conformation. Proc Natl Acad Sci U S A, 102, 17969-17974. PubMed id: 16326809 DOI: 10.1073/pnas.0506039102
Date:
01-Sep-05     Release date:   13-Dec-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P68187  (MALK_ECOLI) -  Maltose/maltodextrin import ATP-binding protein MalK
Seq:
Struc:
371 a.a.
372 a.a.
Protein chain
Pfam   ArchSchema ?
P68187  (MALK_ECOLI) -  Maltose/maltodextrin import ATP-binding protein MalK
Seq:
Struc:
371 a.a.
299 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.3.6.3.19  - Maltose-transporting ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + maltose(Out) = ADP + phosphate + maltose(In)
ATP
+ H(2)O
+ maltose(Out)
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
+ maltose(In)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     metabolic process   7 terms 
  Biochemical function     transporter activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0506039102 Proc Natl Acad Sci U S A 102:17969-17974 (2005)
PubMed id: 16326809  
 
 
ATP hydrolysis is required to reset the ATP-binding cassette dimer into the resting-state conformation.
G.Lu, J.M.Westbrooks, A.L.Davidson, J.Chen.
 
  ABSTRACT  
 
ATP-binding cassette (ABC) transporters couple ATP binding and hydrolysis to the movement of substances across the membrane; conformational changes clearly play an important role in the transporter mechanism. Previously, we have shown that a dimer of MalK, the ATPase subunit of the maltose transporter from Escherichia coli, undergoes a tweezers-like motion in a transport cycle. The MalK monomer consists of an N-terminal nucleotide binding domain and a C-terminal regulatory domain. The two nucleotide-binding domains in a dimer are either open or closed, depending on whether ATP is present, while the regulatory domains maintain contacts to hold the dimer together. In this work, the structure of MalK in a posthydrolysis state is presented, obtained by cocrystallizing MalK with ATP-Mg(2+). ATP was hydrolyzed in the crystallization drop, and ADP-Mg(2+) was found in the resulting crystal structure. In contrast to the ATP-bound form where two ATP molecules are buried in a closed interface between the nucleotide-binding domains, the two nucleotide-binding domains of the ADP-bound form are open, indicating that ADP, unlike ATP, cannot stabilize the closed form. This conclusion is further supported by oligomerization studies of MalK in solution. At low protein concentrations, ATP promotes dimerization of MalK, whereas ADP does not. The structures of dimeric MalK in the nucleotide-free, ATP-bound, and ADP-bound forms provide a framework for understanding the nature of the conformational changes that occur in an ATP-binding cassette transporter hydrolysis cycle, as well as how conformational changes in MalK are coupled to solute transport.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Ribbon diagram of the structure of E. coli. MalK homodimer with bound ADP-Mg2+.(A) Schematic diagram showing the subunit structure of a monomer. The NBD (residues 1-235) is in green/cyan and RD (residues 236-371) in yellow. Different colors further distinguish the subdomains or segments in the NBD as follows: green, RecA-like subdomain (residues 1-87 and 152-235); cyan, helical subdomain (residues 88-151). (B) Stereoview of the homodimer viewed down the local twofold axis. ADP is represented in ball-and-stick model (O atoms, red; N atoms, blue; C atoms, yellow; P atoms, orange; and magnesium, purple). Walker A motif is colored in red. The color schemes for the domains of the two monomers are similar, except that one is rendered in lighter color. (C) Stereoview of the homodimer obtained by a 90° clockwise rotation of the structure shown in B about a horizontal axis. Missing residues are shown as dashed lines. Figures were prepared with PYMOL (www.pymol.
Figure 3.
Fig. 3. ADP binding. (A) Stereoview of the electron density (2 contour level) of one of the bound ADP-Mg2+ obtained from a simulated annealing F[o] - F[c] map, with ADP-Mg2+ molecules omitted in the structure factor calculation. The ADP-Mg2+ is represented in ball-and-stick model. Water molecules are colored in pink. To illustrate that there is no density in the expected position of the phosphate, the ATP molecule also is shown in gray. The ATP model was obtained by aligning the Walker A motif of the ATP-bound form (12) with that of the ADP-bound form. (B) Atomic details of the interaction between MalK and ADP-Mg2+. Residues contacting the ADP and magnesium ion are labeled. Hydrogen-bonding and salt-bridge interactions are marked by dashed lines in orange and blue, respectively. Color identification for the residues is as follows: O atoms, red; N atoms, blue; C atoms, gray; and P and S atoms, orange.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21315686 R.Yang, Y.X.Hou, C.A.Campbell, K.Palaniyandi, Q.Zhao, A.J.Bordner, and X.B.Chang (2011).
Glutamine residues in Q-loops of multidrug resistance protein MRP1 contribute to ATP binding via interaction with metal cofactor.
  Biochim Biophys Acta, 1808, 1790-1796.  
20497229 T.Eitinger, D.A.Rodionov, M.Grote, and E.Schneider (2011).
Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions.
  FEMS Microbiol Rev, 35, 3.  
20061384 A.Siarheyeva, R.Liu, and F.J.Sharom (2010).
Characterization of an asymmetric occluded state of P-glycoprotein with two bound nucleotides: implications for catalysis.
  J Biol Chem, 285, 7575-7586.  
20659291 E.Bordignon, M.Grote, and E.Schneider (2010).
The maltose ATP-binding cassette transporter in the 21st century--towards a structural dynamic perspective on its mode of action.
  Mol Microbiol, 77, 1354-1366.  
19996093 J.W.Weng, K.N.Fan, and W.N.Wang (2010).
The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations.
  J Biol Chem, 285, 3053-3063.  
  20421370 M.F.Tsai, M.Li, and T.C.Hwang (2010).
Stable ATP binding mediated by a partial NBD dimer of the CFTR chloride channel.
  J Gen Physiol, 135, 399-414.  
20154136 V.Eckey, D.Weidlich, H.Landmesser, U.Bergmann, and E.Schneider (2010).
The second extracellular loop of pore-forming subunits of ATP-binding cassette transporters for basic amino acids plays a crucial role in interaction with the cognate solute binding protein(s).
  J Bacteriol, 192, 2150-2159.  
19630440 A.D.Gould, P.G.Telmer, and B.H.Shilton (2009).
Stimulation of the maltose transporter ATPase by unliganded maltose binding protein.
  Biochemistry, 48, 8051-8061.  
19339978 D.C.Gadsby (2009).
Ion channels versus ion pumps: the principal difference, in principle.
  Nat Rev Mol Cell Biol, 10, 344-352.  
  19729090 D.Kaur, M.E.Guerin, H.Skovierová, P.J.Brennan, and M.Jackson (2009).
Chapter 2: Biogenesis of the cell wall and other glycoconjugates of Mycobacterium tuberculosis.
  Adv Appl Microbiol, 69, 23-78.  
19250913 D.Khare, M.L.Oldham, C.Orelle, A.L.Davidson, and J.Chen (2009).
Alternating access in maltose transporter mediated by rigid-body rotations.
  Mol Cell, 33, 528-536.
PDB code: 3fh6
19308707 E.Kinoshita, E.van der Linden, H.Sanchez, and C.Wyman (2009).
RAD50, an SMC family member with multiple roles in DNA break repair: how does ATP affect function?
  Chromosome Res, 17, 277-288.  
18955484 H.T.Lin, V.N.Bavro, N.P.Barrera, H.M.Frankish, S.Velamakanni, H.W.van Veen, C.V.Robinson, M.I.Borges-Walmsley, and A.R.Walmsley (2009).
MacB ABC Transporter Is a Dimer Whose ATPase Activity and Macrolide-binding Capacity Are Regulated by the Membrane Fusion Protein MacA.
  J Biol Chem, 284, 1145-1154.  
19254551 J.Weng, J.Ma, K.Fan, and W.Wang (2009).
Asymmetric conformational flexibility in the ATP-binding cassette transporter HI1470/1.
  Biophys J, 96, 1918-1930.  
19395376 M.Grote, Y.Polyhach, G.Jeschke, H.J.Steinhoff, E.Schneider, and E.Bordignon (2009).
Transmembrane signaling in the maltose ABC transporter MalFGK2-E: periplasmic MalF-P2 loop communicates substrate availability to the ATP-bound MalK dimer.
  J Biol Chem, 284, 17521-17526.  
19047355 M.L.Daus, M.Grote, and E.Schneider (2009).
The MalF P2 loop of the ATP-binding cassette transporter MalFGK2 from Escherichia coli and Salmonella enterica serovar typhimurium interacts with maltose binding protein (MalE) throughout the catalytic cycle.
  J Bacteriol, 191, 754-761.  
19748342 S.Newstead, P.W.Fowler, P.Bilton, E.P.Carpenter, P.J.Sadler, D.J.Campopiano, M.S.Sansom, and S.Iwata (2009).
Insights into how nucleotide-binding domains power ABC transport.
  Structure, 17, 1213-1222.
PDB code: 3fvq
19691360 Y.X.Hou, C.Z.Li, K.Palaniyandi, P.M.Magtibay, L.Homolya, B.Sarkadi, and X.B.Chang (2009).
Effects of putative catalytic base mutation E211Q on ABCG2-mediated methotrexate transport.
  Biochemistry, 48, 9122-9131.  
18452585 A.K.Mishra, L.J.Alderwick, D.Rittmann, C.Wang, A.Bhatt, W.R.Jacobs, K.Takayama, L.Eggeling, and G.S.Besra (2008).
Identification of a novel alpha(1-->6) mannopyranosyltransferase MptB from Corynebacterium glutamicum by deletion of a conserved gene, NCgl1505, affords a lipomannan- and lipoarabinomannan-deficient mutant.
  Mol Microbiol, 68, 1595-1613.  
18535149 A.L.Davidson, E.Dassa, C.Orelle, and J.Chen (2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
  Microbiol Mol Biol Rev, 72, 317.  
18725638 C.Orelle, T.Ayvaz, R.M.Everly, C.S.Klug, and A.L.Davidson (2008).
Both maltose-binding protein and ATP are required for nucleotide-binding domain closure in the intact maltose ABC transporter.
  Proc Natl Acad Sci U S A, 105, 12837-12842.  
17951296 J.Weng, J.Ma, K.Fan, and W.Wang (2008).
The conformational coupling and translocation mechanism of vitamin B12 ATP-binding cassette transporter BtuCD.
  Biophys J, 94, 612-621.  
18567630 M.Grote, E.Bordignon, Y.Polyhach, G.Jeschke, H.J.Steinhoff, and E.Schneider (2008).
A comparative electron paramagnetic resonance study of the nucleotide-binding domains' catalytic cycle in the assembled maltose ATP-binding cassette importer.
  Biophys J, 95, 2924-2938.  
18790847 P.C.Wen, and E.Tajkhorshid (2008).
Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis.
  Biophys J, 95, 5100-5110.  
18088596 R.Yang, R.Scavetta, and X.B.Chang (2008).
The hydroxyl group of S685 in Walker A motif and the carboxyl group of D792 in Walker B motif of NBD1 play a crucial role for multidrug resistance protein folding and function.
  Biochim Biophys Acta, 1778, 454-465.  
18024585 A.Ward, C.L.Reyes, J.Yu, C.B.Roth, and G.Chang (2007).
Flexibility in the ABC transporter MsbA: Alternating access with a twist.
  Proc Natl Acad Sci U S A, 104, 19005-19010.
PDB codes: 3b5w 3b5x 3b5y 3b5z 3b60
18032609 L.Cuthbertson, M.S.Kimber, and C.Whitfield (2007).
Substrate binding by a bacterial ABC transporter involved in polysaccharide export.
  Proc Natl Acad Sci U S A, 104, 19529-19534.
PDB code: 2r5o
17961142 M.L.Daus, S.Berendt, S.Wuttge, and E.Schneider (2007).
Maltose binding protein (MalE) interacts with periplasmic loops P2 and P1 respectively of the MalFG subunits of the maltose ATP binding cassette transporter (MalFGK(2)) from Escherichia coli/Salmonella during the transport cycle.
  Mol Microbiol, 66, 1107-1122.  
18033289 M.L.Oldham, D.Khare, F.A.Quiocho, A.L.Davidson, and J.Chen (2007).
Crystal structure of a catalytic intermediate of the maltose transporter.
  Nature, 450, 515-521.
PDB code: 2r6g
17927448 P.P.Borbat, K.Surendhran, M.Bortolus, P.Zou, J.H.Freed, and H.S.Mchaourab (2007).
Conformational motion of the ABC transporter MsbA induced by ATP hydrolysis.
  PLoS Biol, 5, e271.  
17187755 R.Yang, and X.B.Chang (2007).
Hydrogen-bond formation of the residue in H-loop of the nucleotide binding domain 2 with the ATP in this site and/or other residues of multidrug resistance protein MRP1 plays a crucial role during ATP-dependent solute transport.
  Biochim Biophys Acta, 1768, 324-335.  
  17353351 S.G.Bompadre, Y.Sohma, M.Li, and T.C.Hwang (2007).
G551D and G1349D, two CF-associated mutations in the signature sequences of CFTR, exhibit distinct gating defects.
  J Gen Physiol, 129, 285-298.  
18058211 Z.E.Sauna, I.W.Kim, and S.V.Ambudkar (2007).
Genomics and the mechanism of P-glycoprotein (ABCB1).
  J Bioenerg Biomembr, 39, 481-487.  
17029409 A.H.Buchaklian, and C.S.Klug (2006).
Characterization of the LSGGQ and H motifs from the Escherichia coli lipid A transporter MsbA.
  Biochemistry, 45, 12539-12546.  
16929303 C.B.Andersen, T.Becker, M.Blau, M.Anand, M.Halic, B.Balar, T.Mielke, T.Boesen, J.S.Pedersen, C.M.Spahn, T.G.Kinzy, G.R.Andersen, and R.Beckmann (2006).
Structure of eEF3 and the mechanism of transfer RNA release from the E-site.
  Nature, 443, 663-668.
PDB codes: 2iw3 2iwh 2ix3 2ix8
16829526 D.L.Croteau, M.J.DellaVecchia, H.Wang, R.J.Bienstock, M.A.Melton, and B.Van Houten (2006).
The C-terminal zinc finger of UvrA does not bind DNA directly but regulates damage-specific DNA binding.
  J Biol Chem, 281, 26370-26381.  
17215877 E.O.Oloo, C.Kandt, M.L.O'Mara, and D.P.Tieleman (2006).
Computer simulations of ABC transporter components.
  Biochem Cell Biol, 84, 900-911.  
16858415 J.Zaitseva, C.Oswald, T.Jumpertz, S.Jenewein, A.Wiedenmann, I.B.Holland, and L.Schmitt (2006).
A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer.
  EMBO J, 25, 3432-3443.
PDB codes: 2ff7 2ffa 2ffb 2fgj 2fgk
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.