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(-) Description

Title :  CRYSTAL STRUCTURE OF SUBUNIT B MUTANT N157A OF THE A1AO ATP SYNTHASE
 
Authors :  V. S. Tadwal, M. S. S. Manimekalai, J. Jeyakanthan, G. Gruber
Date :  22 Aug 11  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Atp Synthesis, Hydrogen Ion Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. S. Tadwal, M. S. S. Manimekalai, G. Gruber
Structure Of Subunit A Mutants H156A, N157A And N157T Of Th A1Ao Atp Synthase
To Be Published
PubMed: search
(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: AHAB, ATPB, MM_0779
    Mutation: YES
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 192952
    Strain: GO1
    Synonym: V-ATPASE SUBUNIT B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2AES1Ligand/Ion4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
3CL1Ligand/IonCHLORIDE ION
4GOL11Ligand/IonGLYCEROL
5PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
6PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:137 , ASN A:138 , SER A:346 , MET A:351 , SER A:368 , ASP A:369 , TYR A:372 , HOH A:806 , HOH A:807 , HOH A:809 , ARG B:349BINDING SITE FOR RESIDUE GOL A 461
02AC2SOFTWARELYS A:124 , ASP A:125 , ARG A:142 , HIS A:241 , ALA A:293 , HOH A:818BINDING SITE FOR RESIDUE GOL A 462
03AC3SOFTWAREARG A:87 , ASP A:97 , LYS A:447BINDING SITE FOR RESIDUE GOL A 463
04AC4SOFTWAREPHE A:149 , SER A:150 , MET A:305 , VAL A:328 , ALA A:329 , ARG A:330 , ASP B:316BINDING SITE FOR RESIDUE GOL A 464
05AC5SOFTWAREILE A:185 , THR A:186 , ASN A:187 , GLU A:188 , LEU A:212 , ALA A:213 , ASP A:214 , HOH A:1105BINDING SITE FOR RESIDUE GOL A 465
06AC6SOFTWARELEU B:384 , ALA B:392 , LEU B:393 , SER B:394 , ASP B:397BINDING SITE FOR RESIDUE GOL A 466
07AC7SOFTWAREGLY A:35 , MET A:115 , HOH A:492 , HOH A:591 , TYR B:236BINDING SITE FOR RESIDUE PG0 A 6108
08AC8SOFTWAREMET A:115 , ASN A:116 , TYR A:236 , LYS A:291 , HOH A:678 , MET B:115 , ASN B:116 , TYR B:236 , LYS B:291BINDING SITE FOR RESIDUE GOL A 467
09AC9SOFTWARELYS A:20 , GLU A:22 , PRO A:23 , ALA A:49 , GLU B:204 , ARG B:205 , HOH B:553BINDING SITE FOR RESIDUE GOL A 468
10BC1SOFTWAREARG A:349 , THR B:137 , ASN B:138 , SER B:346 , SER B:368 , ASP B:369 , TYR B:372 , HOH B:472 , HOH B:473 , HOH B:728 , HOH B:814 , HOH B:873BINDING SITE FOR RESIDUE GOL B 461
11BC2SOFTWARELYS B:124 , ASP B:125 , ARG B:142 , HIS B:241 , ALA B:293 , HOH B:715 , HOH B:798BINDING SITE FOR RESIDUE GOL B 462
12BC3SOFTWAREPHE A:149 , SER A:318 , ILE A:321 , GLN A:325 , PHE B:149 , GLN B:325 , HOH B:525 , HOH B:526 , HOH B:938BINDING SITE FOR RESIDUE PG4 B 6112
13BC4SOFTWAREGLY A:336 , ASP A:409 , ARG A:413 , HOH A:1026 , HOH A:1027 , LYS B:20 , PRO B:23 , VAL B:24 , TYR B:26 , SER B:47 , SER B:48 , 1PE B:463BINDING SITE FOR RESIDUE AES B 1474
14BC5SOFTWAREGLU A:158 , TYR A:192 , HIS A:333 , GLY A:336 , HOH A:714 , HOH A:825 , HOH A:875 , HOH A:1003 , LYS B:20 , THR B:21 , GLU B:22 , PRO B:23 , AES B:1474BINDING SITE FOR RESIDUE 1PE B 463
15BC6SOFTWAREHIS B:156 , ALA B:157 , GLU B:189 , THR B:247 , ASP B:248 , HOH B:482 , HOH B:509 , HOH B:510 , HOH B:511BINDING SITE FOR RESIDUE GOL B 464
16BC7SOFTWAREASP A:316 , HOH A:802 , HOH A:803 , ARG B:334BINDING SITE FOR RESIDUE CL B 465

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:247 -Asp A:248
2Tyr A:338 -Pro A:339
3Thr B:247 -Asp B:248
4Tyr B:338 -Pro B:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 3TIV)

(-) 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:437
 aligned with VATB_METMA | Q60187 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:446
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
           VATB_METMA    12 AGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEGTGGLDKDCGVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeee.....eeeeeeeee...eeeeee...---------..eeee..eeeehhhhh.eeee...............eeee..............eee....hhhhhh....ee.....eeee...hhhhhhhhhhhhh........eeeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhh..........hhhhhhhhhhhh..ee......eeeeeeeeee..........hhhhhh..eeee.hhhhhhh...........ee.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tiv A  12 AGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEG---------VIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHAEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 457
                                    21        31        41        51       | -       |71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
                                                                          59        69                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:430
 aligned with VATB_METMA | Q60187 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:450
                                    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       460
           VATB_METMA    11 IAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEGTGGLDKDCGVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHRKAK 460
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.........eeeee.....eeeeeeeee...eeeeee..---------....eee..eeeehhhhh.eeee...............eeee..............eee....hhhhhh....ee.....eeee...hhhhhhhhhhhhh........eeeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhh.-----------....hhhhhhhhhhh..ee......eeeeeeeeee...........hhhhh..eeee.hhhhhhh...........ee.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tiv B  11 IAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFE---------GVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHAEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQM-----------GYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHRKAK 460
                                    20        30        40        50       | -       |70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        |-         -|      280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460
                                                                          58        68                                                                                                                                                                                            259         271
   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 3TIV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2c61 2rkw 3dsr 3eiu 3ssa 3tgw