spacer
spacer

PDBsum entry 3b8c

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
3b8c
Jmol
Contents
Protein chains
833 a.a. *
Ligands
ACP ×2
Metals
_MG ×2
* Residue conservation analysis
PDB id:
3b8c
Name: Hydrolase
Title: Crystal structure of a plasma membrane proton pump
Structure: Atpase 2, plasma membrane-type. Chain: a, b. Fragment: aha2delta73 c-terminal truncated. Synonym: proton pump 2, aha2. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: aha2. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Resolution:
3.60Å     R-factor:   0.351     R-free:   0.366
Authors: B.P.Pedersen,M.J.Buch-Pedersen,J.P.Morth,M.G.Palmgren, P.Nissen
Key ref:
B.P.Pedersen et al. (2007). Crystal structure of the plasma membrane proton pump. Nature, 450, 1111-1114. PubMed id: 18075595 DOI: 10.1038/nature06417
Date:
01-Nov-07     Release date:   18-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P19456  (PMA2_ARATH) -  ATPase 2, plasma membrane-type
Seq:
Struc:
 
Seq:
Struc:
948 a.a.
833 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.3.6  - Proton-exporting ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + H+(In) = ADP + phosphate + H+(Out)
ATP
+ H(2)O
+ H(+)(In)
=
ADP
Bound ligand (Het Group name = ACP)
matches with 81.00% similarity
+ phosphate
+ H(+)(Out)
      Cofactor: Mg(2+)
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     transport   5 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1038/nature06417 Nature 450:1111-1114 (2007)
PubMed id: 18075595  
 
 
Crystal structure of the plasma membrane proton pump.
B.P.Pedersen, M.J.Buch-Pedersen, J.P.Morth, M.G.Palmgren, P.Nissen.
 
  ABSTRACT  
 
A prerequisite for life is the ability to maintain electrochemical imbalances across biomembranes. In all eukaryotes the plasma membrane potential and secondary transport systems are energized by the activity of P-type ATPase membrane proteins: H+-ATPase (the proton pump) in plants and fungi, and Na+,K+-ATPase (the sodium-potassium pump) in animals. The name P-type derives from the fact that these proteins exploit a phosphorylated reaction cycle intermediate of ATP hydrolysis. The plasma membrane proton pumps belong to the type III P-type ATPase subfamily, whereas Na+,K+-ATPase and Ca2+-ATPase are type II. Electron microscopy has revealed the overall shape of proton pumps, however, an atomic structure has been lacking. Here we present the first structure of a P-type proton pump determined by X-ray crystallography. Ten transmembrane helices and three cytoplasmic domains define the functional unit of ATP-coupled proton transport across the plasma membrane, and the structure is locked in a functional state not previously observed in P-type ATPases. The transmembrane domain reveals a large cavity, which is likely to be filled with water, located near the middle of the membrane plane where it is lined by conserved hydrophilic and charged residues. Proton transport against a high membrane potential is readily explained by this structural arrangement.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Overall structure of the plasma membrane H^+-ATPase. The structure represents an active form of the proton pump, without its auto-inhibitory C terminus, in complex with Mg-AMPPCP. Ten transmembrane helices, orange, green and brown, as indicated; nucleotide-binding domain (N), red; the phosphorylation domain (P), blue; and the actuator domain (A), yellow. Mg-AMPPCP is found at the interface between the N and P domains and is shown as a ball-and-stick reprentation. Key residues mentioned in the text are shown as sticks. The grey box depicts the approximate location of the plasma membrane.
Figure 4.
Figure 4: Mechanism of proton transport by plasma membrane H^+-ATPase. E2-model forms of the H^+-ATPase were made by structural alignment of our E1-AMPPCP structure with the E2P structure of the Ca^2+-ATPase^26 and the E2-P* structure (E2 occluded state of the pump) of the Ca^2+-ATPase (PDB code 1XP5). Asp 684 is the central proton donor/acceptor of the pump, and together with Arg 655 it lines a centrally located water-filled cavity. In the E1 conformation, hydrogen bonding between Asp 684 and Asn 106 gives preference to the protonated form of Asp 684 (E1-ATP structure). Conformational movements in the membrane region, coupled to E1–E2 transitions, result in opening of the cavity towards the proton exit pathway (E2P model) and interrupt hydrogen bonding between Asn 106 and Asp 684; this results in proton release from Asp 684, now exposed to the extracellular environment. Placement of Arg 655 towards Asp 684 at the exit channel also stimulates proton release from Asp 684, and provides a positively charged plug in this area of the molecule that prevents extracellular protons from re-protonating Asp 684. At the same time Arg 655 functions as a built-in counter-ion that neutralizes the negative charge on Asp 684 and promotes swift formation of the occluded E2-P* transition state (E2P* model), dephosphorylation and transition to the E2 form.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 450, 1111-1114) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22456709 S.M.Lin, J.Y.Tsai, C.D.Hsiao, Y.T.Huang, C.L.Chiu, M.H.Liu, J.Y.Tung, T.H.Liu, R.L.Pan, and Y.J.Sun (2012).
Crystal structure of a membrane-embedded H+-translocating pyrophosphatase.
  Nature, 484, 399-403.
PDB code: 4a01
  21542031 D.Himmel, S.K.Goll, I.Leito, and I.Krossing (2011).
Anchor Points for the Unified Brønsted Acidity Scale: The rCCC Model for the Calculation of Standard Gibbs Energies of Proton Solvation in Eleven Representative Liquid Media.
  Chemistry, 17, 5808-5826.  
21081109 D.P.Drew, M.Hrmova, C.Lunde, A.K.Jacobs, M.Tester, and G.B.Fincher (2011).
Structural and functional analyses of PpENA1 provide insights into cation binding by type IID P-type ATPases in lower plants and fungi.
  Biochim Biophys Acta, 1808, 1483-1492.  
21210186 D.Raimunda, M.González-Guerrero, B.W.Leeber, and J.M.Argüello (2011).
The transport mechanism of bacterial Cu(+)-ATPases: distinct efflux rates adapted to different function.
  Biometals, 24, 467-475.  
21215281 I.Vandecaetsbeek, S.B.Christensen, H.Liu, P.P.Van Veldhoven, E.Waelkens, J.Eggermont, L.Raeymaekers, J.V.Møller, P.Nissen, F.Wuytack, and P.Vangheluwe (2011).
Thapsigargin affinity purification of intracellular P(2A)-type Ca(2+) ATPases.
  Biochim Biophys Acta, 1813, 1118-1127.  
21179061 J.P.Morth, B.P.Pedersen, M.J.Buch-Pedersen, J.P.Andersen, B.Vilsen, M.G.Palmgren, and P.Nissen (2011).
A structural overview of the plasma membrane Na+,K+-ATPase and H+-ATPase ion pumps.
  Nat Rev Mol Cell Biol, 12, 60-70.  
21396942 K.Walldén, and P.Nordlund (2011).
Structural basis for the allosteric regulation and substrate recognition of human cytosolic 5'-nucleotidase II.
  J Mol Biol, 408, 684-696.
PDB codes: 2xcv 2xcw 2xcx 2xjb 2xjc 2xjd 2xje 2xjf
21351879 M.G.Palmgren, and P.Nissen (2011).
P-type ATPases.
  Annu Rev Biophys, 40, 243-266.  
21156155 M.Miranda, J.P.Pardo, and V.V.Petrov (2011).
Structure-function relationships in membrane segment 6 of the yeast plasma membrane Pma1 H(+)-ATPase.
  Biochim Biophys Acta, 1808, 1781-1789.  
21716286 P.Gourdon, X.Y.Liu, T.Skjørringe, J.P.Morth, L.B.Møller, B.P.Pedersen, and P.Nissen (2011).
Crystal structure of a copper-transporting PIB-type ATPase.
  Nature, 475, 59-64.
PDB code: 3rfu
21194369 R.L.López-Marqués, J.C.Holthuis, and T.G.Pomorski (2011).
Pumping lipids with P4-ATPases.
  Biol Chem, 392, 67-76.  
21187400 T.Jimenez, J.P.McDermott, G.Sánchez, and G.Blanco (2011).
Na,K-ATPase alpha4 isoform is essential for sperm fertility.
  Proc Natl Acad Sci U S A, 108, 644-649.  
21194372 V.H.Lam, J.H.Lee, A.Silverio, H.Chan, K.M.Gomolplitinant, T.L.Povolotsky, E.Orlova, E.I.Sun, C.H.Welliver, and M.H.Saier (2011).
Pathways of transport protein evolution: recent advances.
  Biol Chem, 392, 5.  
20179343 B.P.Pedersen, J.P.Morth, and P.Nissen (2010).
Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history.
  Acta Crystallogr D Biol Crystallogr, 66, 309-313.  
20809990 J.V.Møller, C.Olesen, A.M.Winther, and P.Nissen (2010).
The sarcoplasmic Ca2+-ATPase: design of a perfect chemi-osmotic pump.
  Q Rev Biophys, 43, 501-566.  
21098259 K.Ekberg, B.P.Pedersen, D.M.Sørensen, A.K.Nielsen, B.Veierskov, P.Nissen, M.G.Palmgren, and M.J.Buch-Pedersen (2010).
Structural identification of cation binding pockets in the plasma membrane proton pump.
  Proc Natl Acad Sci U S A, 107, 21400-21405.  
20068040 K.Ekberg, M.G.Palmgren, B.Veierskov, and M.J.Buch-Pedersen (2010).
A novel mechanism of P-type ATPase autoinhibition involving both termini of the protein.
  J Biol Chem, 285, 7344-7350.  
19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
  Eur Biophys J, 39, 723-755.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
19917612 L.Banci, I.Bertini, F.Cantini, S.Inagaki, M.Migliardi, and A.Rosato (2010).
The binding mode of ATP revealed by the solution structure of the N-domain of human ATP7A.
  J Biol Chem, 285, 2537-2544.
PDB codes: 2kmv 2kmx
20634056 M.Bublitz, H.Poulsen, J.P.Morth, and P.Nissen (2010).
In and out of the cation pumps: P-type ATPase structure revisited.
  Curr Opin Struct Biol, 20, 431-439.  
20053675 R.L.López-Marqués, L.R.Poulsen, S.Hanisch, K.Meffert, M.J.Buch-Pedersen, M.K.Jakobsen, T.G.Pomorski, and M.G.Palmgren (2010).
Intracellular targeting signals and lipid specificity determinants of the ALA/ALIS P4-ATPase complex reside in the catalytic ALA alpha-subunit.
  Mol Biol Cell, 21, 791-801.  
  20100892 S.Meier, N.N.Tavraz, K.L.Dürr, and T.Friedrich (2010).
Hyperpolarization-activated inward leakage currents caused by deletion or mutation of carboxy-terminal tyrosines of the Na+/K+-ATPase {alpha} subunit.
  J Gen Physiol, 135, 115-134.  
20192763 W.Yang (2010).
Lessons learned from UvrD helicase: mechanism for directional movement.
  Annu Rev Biophys, 39, 367-385.  
21067515 Y.Chang, J.Wu, X.J.Tong, J.Q.Zhou, and J.Ding (2010).
Crystal structure of the catalytic core of Saccharomyces cerevesiae histone demethylase Rph1: insights into the substrate specificity and catalytic mechanism.
  Biochem J, 433, 295-302.
PDB codes: 3opt 3opw
19181866 C.Sirichandra, A.Wasilewska, F.Vlad, C.Valon, and J.Leung (2009).
The guard cell as a single-cell model towards understanding drought tolerance and abscisic acid action.
  J Exp Bot, 60, 1439-1463.  
19031011 F.A.Hays, Z.Roe-Zurz, M.Li, L.Kelly, F.Gruswitz, A.Sali, and R.M.Stroud (2009).
Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.
  J Struct Funct Genomics, 10, 9.  
18228034 G.Duby, and M.Boutry (2009).
The plant plasma membrane proton pump ATPase: a highly regulated P-type ATPase with multiple physiological roles.
  Pflugers Arch, 457, 645-655.  
19088078 G.Duby, W.Poreba, D.Piotrowiak, K.Bobik, R.Derua, E.Waelkens, and M.Boutry (2009).
Activation of Plant Plasma Membrane H+-ATPase by 14-3-3 Proteins Is Negatively Controlled by Two Phosphorylation Sites within the H+-ATPase C-terminal Region.
  J Biol Chem, 284, 4213-4221.  
19411703 G.Lenoir, P.Williamson, C.F.Puts, and J.C.Holthuis (2009).
Cdc50p plays a vital role in the ATPase reaction cycle of the putative aminophospholipid transporter drs2p.
  J Biol Chem, 284, 17956-17967.  
19074772 I.Mangialavori, A.M.Giraldo, C.M.Buslje, M.F.Gomes, A.J.Caride, and J.P.Rossi (2009).
A new conformation in sarcoplasmic reticulum calcium pump and plasma membrane Ca2+ pumps revealed by a photoactivatable phospholipidic probe.
  J Biol Chem, 284, 4823-4828.  
19564897 J.Liu, J.M.Elmore, A.T.Fuglsang, M.G.Palmgren, B.J.Staskawicz, and G.Coaker (2009).
RIN4 functions with plasma membrane H+-ATPases to regulate stomatal apertures during pathogen attack.
  PLoS Biol, 7, e1000139.  
19387495 K.Abe, K.Tani, T.Nishizawa, and Y.Fujiyoshi (2009).
Inter-subunit interaction of gastric H+,K+-ATPase prevents reverse reaction of the transport cycle.
  EMBO J, 28, 1637-1643.
PDB code: 3ixz
19923713 K.O.Håkansson (2009).
The structure of Mg-ATPase nucleotide-binding domain at 1.6 A resolution reveals a unique ATP-binding motif.
  Acta Crystallogr D Biol Crystallogr, 65, 1181-1186.
PDB code: 3gwi
19548020 M.D.Thever, and M.H.Saier (2009).
Bioinformatic characterization of p-type ATPases encoded within the fully sequenced genomes of 26 eukaryotes.
  J Membr Biol, 229, 115-130.  
20040113 M.Freigassner, H.Pichler, and A.Glieder (2009).
wTuning microbial hosts for membrane protein production.
  Microb Cell Fact, 8, 69.  
18458946 M.J.Buch-Pedersen, B.P.Pedersen, B.Veierskov, P.Nissen, and M.G.Palmgren (2009).
Protons and how they are transported by proton pumps.
  Pflugers Arch, 457, 573-579.  
19061901 M.Li, F.A.Hays, Z.Roe-Zurz, L.Vuong, L.Kelly, C.M.Ho, R.M.Robbins, U.Pieper, J.D.O'Connell, L.J.Miercke, K.M.Giacomini, A.Sali, and R.M.Stroud (2009).
Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.
  J Mol Biol, 385, 820-830.  
19494845 P.Nissen (2009).
One way for the gastric proton pump.
  EMBO J, 28, 1535-1536.  
19834508 T.Boesen, and P.Nissen (2009).
V for victory--a V1-ATPase structure revealed.
  EMBO Rep, 10, 1211-1212.  
19478797 T.Tsuda, and C.Toyoshima (2009).
Nucleotide recognition by CopA, a Cu+-transporting P-type ATPase.
  EMBO J, 28, 1782-1791.
PDB codes: 3a1c 3a1d 3a1e
19916929 V.V.Petrov (2009).
Functioning of Saccharomyces cerevisiae Pma1 H+-ATPase carrying the minimal number of cysteine residues.
  Biochemistry (Mosc), 74, 1155-1163.  
19360018 Z.E.Newby, J.D.O'Connell, F.Gruswitz, F.A.Hays, W.E.Harries, I.M.Harwood, J.D.Ho, J.K.Lee, D.F.Savage, L.J.Miercke, and R.M.Stroud (2009).
A general protocol for the crystallization of membrane proteins for X-ray structural investigation.
  Nat Protoc, 4, 619-637.  
18547529 C.C.Wu, W.J.Rice, and D.L.Stokes (2008).
Structure of a copper pump suggests a regulatory role for its metal-binding domain.
  Structure, 16, 976-985.
PDB code: 2voy
18451787 D.Drew, S.Newstead, Y.Sonoda, H.Kim, G.von Heijne, and S.Iwata (2008).
GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae.
  Nat Protoc, 3, 784-798.  
18674618 E.P.Carpenter, K.Beis, A.D.Cameron, and S.Iwata (2008).
Overcoming the challenges of membrane protein crystallography.
  Curr Opin Struct Biol, 18, 581-586.  
18707888 E.Padan (2008).
The enlightening encounter between structure and function in the NhaA Na+-H+ antiporter.
  Trends Biochem Sci, 33, 435-443.  
18403373 M.Morii, M.Yamauchi, T.Ichikawa, T.Fujii, Y.Takahashi, S.Asano, N.Takeguchi, and H.Sakai (2008).
Involvement of the H3O+-Lys-164 -Gln-161-Glu-345 charge transfer pathway in proton transport of gastric H+,K+-ATPase.
  J Biol Chem, 283, 16876-16884.  
18581035 P.L.Jorgensen (2008).
Importance for absorption of Na+ from freshwater of lysine, valine and serine substitutions in the alpha1a-isoform of Na,K-ATPase in the gills of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar).
  J Membr Biol, 223, 37-47.  
18343670 V.Niggli, and E.Sigel (2008).
Anticipating antiport in P-type ATPases.
  Trends Biochem Sci, 33, 156-160.  
18075569 D.C.Gadsby (2007).
Structural biology: ion pumps made crystal clear.
  Nature, 450, 957-959.  
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.