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(-) Description

Title :  INTERMEDIATE POSITION OF ATP ON ITS TRAIL TO THE BINDING POCKET INSIDE THE SUBUNIT B MUTANT R416W OF THE ENERGY CONVERTER A1AO ATP SYNTHASE
 
Authors :  A. Kumar, M. S. S. Manimekalai, A. M. Balakrishna, C. Hunke, G. Gruber
Date :  18 Oct 07  (Deposition) - 09 Sep 08  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Atp Synthesis, Hydrogen Ion Transport, Ion Transport, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, M. S. S. Manimekalai, A. M. Balakrishna, C. Hunke, S. Weigelt, N. Sewald, G. Gruber
Spectroscopic And Crystallographic Studies Of The Mutant R416W Give Insight Into The Nucleotide Binding Traits Of Subunit B Of The A1Ao Atp Synthase
Proteins V. 75 807 2009
PubMed-ID: 19003877  |  Reference-DOI: 10.1002/PROT.22289
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - V-TYPE ATP SYNTHASE BETA CHAIN
    Chains: A, B
    EC Number: 3.6.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9D-HIS6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ATPB
    Mutation: YES
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209
    Strain: GO1
    Synonym: V-TYPE ATPASE SUBUNIT B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2RKW)

(-) Sites  (0, 0)

(no "Site" information available for 2RKW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RKW)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Gly A:98 -Gly A:99
2Met A:115 -Asn A:116
3Thr A:247 -Asp A:248
4Tyr A:272 -Pro A:273
5Ile A:314 -Pro A:315
6Tyr A:338 -Pro A:339
7Pro A:339 -Pro A:340
8Phe B:71 -Thr B:72
9Thr B:72 -Gly B:73
10Gly B:260 -Ala B:261
11His B:312 -Pro B:313
12Tyr B:338 -Pro B:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RKW)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATPASE_ALPHA_BETAPS00152 ATP synthase alpha and beta subunits signature.VATB_METMA339-348
 		  2A:339-348
B:339-348

(-) Exons   (0, 0)

(no "Exon" information available for 2RKW)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:422
 aligned with VATB_METMA | Q60187 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:447
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       
           VATB_METMA    11 IAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEGTGGLDKDCGVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..........ee...........eeeeee....eee.--------------.......eeeehhhhh..ee................eeee.....................hhhhhh...........eeee...hhhhhhhhhhhhh........eeeeeeeeeehhhhhhhhhhhhhhh.hhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhh...-----------........hhhhhh..ee......eeeeeeeeee...........hhhhh..eeee.hhhhhh............ee.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh........hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rkw A  11 IAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQ--------------IFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMG-----------YPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGWNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
                                    20        30        40        50    |    -        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         - |     280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       
                                                                       55             70                                                                                                                                                                                           260         272                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:422
 aligned with VATB_METMA | Q60187 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:448
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449        
           VATB_METMA    10 QIAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEGTGGLDKDCGVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ATP-synt_ab_N-2rkwB01 B:10-73                                   -------------------------------------------------------ATP-synt_ab-2rkwB03 B:129-348                                                                                                                                                                                               ----------------ATP-synt_ab_C-2rkwB05 B:365-457                                                               Pfam domains (1)
           Pfam domains (2) ATP-synt_ab_N-2rkwB02 B:10-73                                   -------------------------------------------------------ATP-synt_ab-2rkwB04 B:129-348                                                                                                                                                                                               ----------------ATP-synt_ab_C-2rkwB06 B:365-457                                                               Pfam domains (2)
         Sec.struct. author .......eee..........................ee...eee.....------------......eeeehhhhh..ee................eeee.....................hhhhhh...........ee.......hhhhhhhh...........eeeeeeeeee...hhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh.....--------------....hhhhhh..ee......eeeeeeee....................eeee.hhhhhhh...........ee.hhhhh........hhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rkw B  10 QIAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFE------------FTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGA--------------MYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGWNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
                                    19        29        39        49        |-         - |      79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259 |       -      |279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449        
                                                                           58           71                                                                                                                                                                                           261            276
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2RKW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RKW)

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: HAS-barrel (27)
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: ATP-synt_ab_C] (32)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VATB_METMA | Q60187)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016820    hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances    Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
    GO:0046933    proton-transporting ATP synthase activity, rotational mechanism    Catalysis of the transfer of protons from one side of a membrane to the other according to the reaction: ADP + H2O + phosphate + H+(in) = ATP + H+(out), by a rotational mechanism.
biological process
    GO:0006754    ATP biosynthetic process    The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0015991    ATP hydrolysis coupled proton transport    The transport of protons against an electrochemical gradient, using energy from ATP hydrolysis.
    GO:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0015986    ATP synthesis coupled proton transport    The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0042777    plasma membrane ATP synthesis coupled proton transport    The transport of protons across the plasma membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis.
    GO:0015992    proton transport    The directed movement of protons (hydrogen ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0033178    proton-transporting two-sector ATPase complex, catalytic domain    A protein complex that forms part of a proton-transporting two-sector ATPase complex and catalyzes ATP hydrolysis or synthesis. The catalytic domain (F1, V1, or A1) comprises a hexameric catalytic core and a central stalk, and is peripherally associated with the membrane when the two-sector ATPase is assembled.

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    Gly A:98 - Gly A:99   [ RasMol ]  
    Gly B:260 - Ala B:261   [ RasMol ]  
    His B:312 - Pro B:313   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VATB_METMA | Q60187: 2c61 3b2q 3dsr 3eiu 3ssa 3tgw 3tiv

(-) Related Entries Specified in the PDB File

3b2q