3B2Q - JenaLib

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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 :   19 Oct 07 (Deposition) - 09 Sep 08 (Release) - 16 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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)

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

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	AES	1	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	CIT	1	Ligand/Ion	CITRIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:149 , ALA A:151 , SER A:318 , ILE A:321 , GLN A:325 , VAL A:327 , VAL A:328 , ALA A:329 , ARG A:330 , PRO A:345 , PHE B:149 , ILE B:314 , PRO B:315 , ASP B:316 , SER B:318 , GLN B:325 , HOH B:889	BINDING SITE FOR RESIDUE ATP A 461
2	AC2	SOFTWARE	ARG A:413 , HOH A:463 , HOH A:557 , LYS B:20 , PRO B:23 , VAL B:24 , TYR B:26 , ASP B:46 , SER B:47 , CIT B:463	BINDING SITE FOR RESIDUE AES B 462
3	AC3	SOFTWARE	HIS A:333 , GLY A:336 , HOH A:520 , LYS B:20 , AES B:462 , HOH B:1079 , HOH B:1137	BINDING SITE FOR RESIDUE CIT B 463

(no "SS Bond" information available for 3B2Q)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:247	-	Asp A:248
2	Tyr A:338	-	Pro A:339
3	Gly B:13	-	Pro B:14
4	Thr B:247	-	Asp B:248
5	Tyr B:338	-	Pro B:339

(no "SAP(SNP)/Variant" information available for 3B2Q)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATPASE_ALPHA_BETA	PS00152	ATP synthase alpha and beta subunits signature.	VATB_METMA	339-348	2	A:339-348 B:339-348

(no "Exon" information available for 3B2Q)

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:436
 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 ....eeeee.........eeeee.....eeeeeeeee...eeeeee..-----------..eee..eeeehhhhh.eeee...............eeee.....................hhhhhh...........eeee...hhhhhhhhhhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..ee......eeeeeeeeee...........hhhhh..eeee.hhhhhhh...........ee.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b2q A  11 IAGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFE-----------IFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGWNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHR 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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       
                                                                          58          70

Chain B from PDB  Type:PROTEIN  Length:431
 aligned with VATB_METMA | Q60187 from UniProtKB/Swiss-Prot  Length:460

    Alignment length:449
                                    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 AGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFEGTGGLDKDCGVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGRNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHRKAK 460
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeee.....eeeeeeeee...eeeeee..---------....eee..eeeehhhhh..eee...............eeee.....................hhhhhh...........eeee...hhhhhhhhhhhhh.......eeeeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhh..---------.....hhhhhhhhhhh..ee......eeeeeeeeee...........hhhhh..eeee.hhhhhhh...........ee.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b2q B  12 AGPLIFVEKTEPVGYNEIVNIKMGDGTVRRGQVLDSSADIVVVQVFE---------GVIFTGETLKLPASVDLLGRILSGSGEPRDGGPRIVPDQLLDINGAAMNPYARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLADDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMG---------RGYPGYMYTDLATLYERAGIVKGAKGSVTQIPILSMPGDDITHPIPDLSGYITEGQIVVARELHRKGIYPPINVLPSLSRLMNSGIGAGKTREDHKAVSDQMYAGYAEGRDLRGLVAIVGKEALSERDTKFLEFADLFEDKFVRQGWNENRTIEDTLEIGWQILTHLPENQLGRIDNKYIQKYHPAHRKAK 460
                                    21        31        41        51      |  -      | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        |-       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451         
                                                                         58        68                                                                                                                                                                                             260       270

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 '\|'

(no "SCOP Domain" information available for 3B2Q)

(no "CATH Domain" information available for 3B2Q)

(no "Pfam Domain" information available for 3B2Q)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly B:13 - Pro B:14	[ RasMol ]
		Thr A:247 - Asp A:248	[ RasMol ]
		Thr B:247 - Asp B:248	[ RasMol ]
		Tyr A:338 - Pro A:339	[ RasMol ]
		Tyr B:338 - Pro B:339	[ RasMol ]

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	3b2q
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	VATB_METMA \| Q60187	:	2c61 2rkw 3dsr 3eiu 3ssa 3tgw 3tiv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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