3I72 - JenaLib

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Title :   STRUCTURAL CHARACTERIZATION FOR THE NUCLEOTIDE BINDING ABILITY OF SUBUNIT A WITH SO4 OF THE A1AO ATP SYNTHASE

Authors :   S. M. S. Manimekalai, A. Kumar, A. M. Balakrishna, G. Gruber

Date :   07 Jul 09 (Deposition) - 12 Jan 10 (Release) - 13 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.47

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Atp Synthesis, Atp-Binding, Autocatalytic Cleavage, Hydrogen Ion Transport, Intron Homing, Ion Transport, Nuclease, Nucleotide-Binding, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kumar, M. S. Manimekalai, A. M. Balakrishna, J. Jeyakanthan, G. Gruber
Nucleotide Binding States Of Subunit A Of The A-Atp Synthas And The Implication Of P-Loop Switch In Evolution.
J. Mol. Biol. V. 396 301 2010
PubMed-ID: 19944110 | Reference-DOI: 10.1016/J.JMB.2009.11.046
(for further references see the PDB file header)

Molecule 1 - A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A
	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	:	UNP RESIDUES 1-240, 617-964
	Gene	:	ATPA, PH1975
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	V-TYPE ATP SYNTHASE ALPHA CHAIN, V-ATPASE SUBUNIT A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 6)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	1	Ligand/Ion	SULFATE ION
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:754 , HOH A:771 , HOH A:885 , HOH A:896	BINDING SITE FOR RESIDUE SO4 A 592
2	AC2	SOFTWARE	ILE A:184 , GLU A:581	BINDING SITE FOR RESIDUE TRS A 593
3	AC3	SOFTWARE	GLU A:161 , ALA A:163 , VAL A:173	BINDING SITE FOR RESIDUE ACY A 594
4	AC4	SOFTWARE	GLN A:246 , LYS A:249 , VAL A:479	BINDING SITE FOR RESIDUE MPD A 589
5	AC5	SOFTWARE	MET A:458 , LYS A:461 , LEU A:528 , ASP A:532 , HOH A:774	BINDING SITE FOR RESIDUE MPD A 590
6	AC6	SOFTWARE	ASP A:420 , LEU A:421 , TRP A:432 , LEU A:433 , HOH A:688 , HOH A:720	BINDING SITE FOR RESIDUE MPD A 591

(no "SS Bond" information available for 3I72)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:234	-	Pro A:235
2	Phe A:427	-	Pro A:428

(no "SAP(SNP)/Variant" information available for 3I72)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTEIN_C_TER	PS50818	Intein C-terminal splicing motif profile.	VATA_PYRHO	594-617	1	A:241-241
2	ATPASE_ALPHA_BETA	PS00152	ATP synthase alpha and beta subunits signature.	VATA_PYRHO	804-813	1	A:428-437

(no "Exon" information available for 3I72)

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:514
 aligned with VATA_PYRHO | O57728 from UniProtKB/Swiss-Prot  Length:964

    Alignment length:904
                                    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       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960    
           VATA_PYRHO    61 PGEPVVGTGASLSVELGPGLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSGKCVDGDTLVLTKEFGLIKIKELYEKLDGKGRKIVEGNEEWTELEKPITVYGYKDGKIVEIKATHVYKGVSSGMVEIRTRTGRKIKVTPIHRLFTGRVTKDGLILKEVMAMHVKPGDRIAVVKKIDGGEYIKLDSSNVGEIKVPEILNEELAEFLGYLMANGTLKSGIIEIYCDDESLLERVNSLSLKLFGVGGRIVQKVDGKALVIQSKPLVDVLRRLGVPEDKKVENWKVPRELLLSPSNVVRAFVNAYIKGKEEVEITLASEEGAYELSYLFAKLGIYVTISKSGEYYKVRVSRRGNLDTIPVEVNGMPKVLPYEDFRKFAKSIGLEEVAENHLQHIIFDEVIDVRYIPEPQEVYDVTTETHNFVGGNMPTLLHNTVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 964
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.......eee...............................eeeee......ee....eeeeee.....eeeee......eeeeee...eee......eeee.....eeee...eeee........ee..........hhhhhhhh......eeeee.......----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.hhhhhhhhhh...eeeeeeee......hhhhhh...........hhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........--------------..hhhhhhhhhhhhh..eeee.......eeeeeeeeee........hhhhhhhhhhh.ee...hhhhhhh...........ee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i72 A  61 PGEPVVGTGASLSVELGPRLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSGK----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEAL--------------GYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 588
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -      |244       254       264       274       284       294       304       314       324       334     |   -         -|      364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584    
                                                                                                                                                                                                             240                                                                                                                                                                                                                                                                                                                                                                                      241                                                                                                340            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 '\|'

(no "SCOP Domain" information available for 3I72)

(no "CATH Domain" information available for 3I72)

(no "Pfam Domain" information available for 3I72)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:234 - Pro A:235	[ RasMol ]
		Phe A:427 - Pro A:428	[ RasMol ]

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	3i72
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	VATA_PYRHO \| O57728
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	VATA_PYRHO \| O57728	:	1vdz 3i4l 3i73 3ikj 3m4y 3mfy 3nd8 3nd9 3p20 3qg1 3qia 3qjy 3sdz 3se0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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