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(-) Description

Title :  CRYSTAL STRUCTURE OF P-LOOP G239A MUTANT OF SUBUNIT A OF THE A1AO ATP SYNTHASE
 
Authors :  P. Ragunathan, M. S. S. Manimekalai, A. Kumar, J. Jeyakanthan, G. Grube
Date :  24 Jan 11  (Deposition) - 05 Oct 11  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Priya, A. Kumar, M. S. Manimekalai, G. Gruber
Conserved Glycine Residues In The P-Loop Of Atp Synthases Form A Doorframe For Nucleotide Entrance.
J. Mol. Biol. V. 413 657 2011
PubMed-ID: 21925186  |  Reference-DOI: 10.1016/J.JMB.2011.08.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - V-TYPE ATP SYNTHASE ALPHA CHAIN
    Chains: A
    EC Number: 3.6.3.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)-HIS6
    Expression System Strain: BL21 DE3 RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC SUBUNIT A (UNP RESIDUES 1-240, 617-964)
    Gene: ATPA, PH1975
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A, V-ATPASE SUBUNIT A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1ACY6Ligand/IonACETIC ACID
2MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:551BINDING SITE FOR RESIDUE ACY A 589
2AC2SOFTWAREASP A:420 , LEU A:421 , ASN A:431 , TRP A:432 , LEU A:433 , HOH A:604BINDING SITE FOR RESIDUE MPD A 590
3AC3SOFTWARELYS A:533 , GLU A:536BINDING SITE FOR RESIDUE ACY A 591
4AC4SOFTWAREPRO A:200 , TYR A:201 , LYS A:202BINDING SITE FOR RESIDUE MPD A 592
5AC5SOFTWAREGLN A:246 , LYS A:249BINDING SITE FOR RESIDUE MPD A 593
6AC6SOFTWAREASP A:252BINDING SITE FOR RESIDUE ACY A 594
7AC7SOFTWARETYR A:531BINDING SITE FOR RESIDUE ACY A 595
8AC8SOFTWAREGLU A:580BINDING SITE FOR RESIDUE ACY A 596
9AC9SOFTWAREARG A:335BINDING SITE FOR RESIDUE ACY A 597

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QG1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:401 -Pro A:402
2Phe A:427 -Pro A:428

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QG1)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1INTEIN_C_TERPS50818 Intein C-terminal splicing motif profile.VATA_PYRHO594-617  1A:241-241
2ATPASE_ALPHA_BETAPS00152 ATP synthase alpha and beta subunits signature.VATA_PYRHO804-813  1A:428-437

(-) Exons   (0, 0)

(no "Exon" information available for 3QG1)

(-) 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:561
 aligned with VATA_PYRHO | O57728 from UniProtKB/Swiss-Prot  Length:964

    Alignment length:947
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       
           VATA_PYRHO    18 DGMKGAKMYEVVRVGELGLIGEIIRLEGDKAVIQVYEETAGVRPGEPVVGTGASLSVELGPGLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSGKCVDGDTLVLTKEFGLIKIKELYEKLDGKGRKIVEGNEEWTELEKPITVYGYKDGKIVEIKATHVYKGVSSGMVEIRTRTGRKIKVTPIHRLFTGRVTKDGLILKEVMAMHVKPGDRIAVVKKIDGGEYIKLDSSNVGEIKVPEILNEELAEFLGYLMANGTLKSGIIEIYCDDESLLERVNSLSLKLFGVGGRIVQKVDGKALVIQSKPLVDVLRRLGVPEDKKVENWKVPRELLLSPSNVVRAFVNAYIKGKEEVEITLASEEGAYELSYLFAKLGIYVTISKSGEYYKVRVSRRGNLDTIPVEVNGMPKVLPYEDFRKFAKSIGLEEVAENHLQHIIFDEVIDVRYIPEPQEVYDVTTETHNFVGGNMPTLLHNTVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 964
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................................eee................................eeeee......ee....eeeeee.....eeeee......eeeeee...eee......eeee.....eeee...............ee..........hhhhhhhh......eee.........----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.hhhhhhhhhh...eeee.......hhhhhhh.............hhhh.eeee.......hhhhhhhhhhhhhhhhhhhh...eeeee...............----------....hhhhhhhhhhhh.eeee.......eeeeeee............hhhhhhh....ee...hhhhhhh...........ee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qg1 A  18 DGMKGAKMYEVVRVGELGLIGEIIRLEGDKAVIQVYEETAGVRPGEPVVGTGASLSVELGPRLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSAK----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREIS----------GYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 588
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237  |      -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       241       251       261       271       281       291       301       311       321       331       341  |      -   |   361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       
                                                                                                                                                                                                                                                        240                                                                                                                                                                                                                                                                                                                                                                                      241                                                                                                    344        355
   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 3QG1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QG1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QG1)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VATA_PYRHO | O57728)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
    GO:0006314    intron homing    Lateral transfer of an intron to a homologous allele that lacks the intron, mediated by a site-specific endonuclease encoded within the mobile intron.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    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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  VATA_PYRHO | O57728
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 Related Entries

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

UniProtKB/Swiss-Prot
        VATA_PYRHO | O57728: 1vdz 3i4l 3i72 3i73 3ikj 3m4y 3mfy 3nd8 3nd9 3p20 3qia 3qjy 3sdz 3se0

(-) Related Entries Specified in the PDB File

1vdz WILD TYPE PROTEIN
3i42 WILD TYPE PROTEIN COMPLEXED WITH AMP-PNP
3i72 WILD TYPE PROTEIN COMPLEXED WITH SULPHATE
3i73 WILD TYPE PROTEIN COMPLEXED WITH ADP
3ikj S238A MUTANT OF THE SAME PROTEIN
3m4y P235A MUTANT OF THE SAME PROTEIN
3mfy F236A MUTANT OF THE SAME PROTEIN