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Title :   CRYSTAL STRUCTURE OF VANADATE BOUND SUBUNIT A OF THE A1AO ATP SYNTHASE

Authors :   M. S. S. Manimekalai, A. Kumar, J. Jeyakanthan, G. Gruber

Date :   01 Oct 10 (Deposition) - 30 Mar 11 (Release) - 04 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Manimekalai, A. Kumar, J. Jeyakanthan, G. Gruber
The Transition-Like State And Pi Entrance Into The Catalyti A Subunit Of The Biological Engine A-Atp Synthase.
J. Mol. Biol. V. 408 736 2011
PubMed-ID: 21396943 | Reference-DOI: 10.1016/J.JMB.2011.03.010
(for further references see the PDB file header)

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 (UNP RESIDUES 1-240, 617-964)
	Gene	:	ATPA, PH1975
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS HORIKOSHII, PYROCOCCUS HORIKOSHII
	Organism Taxid	:	53953, 53953
	Other Details	:	THE FUSION OF RESIDUES 1-240 AND RESIDUES 617-964 FROM V-ATPASE SUBUNIT A
	Strain	:	OT3
	Synonym	:	A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 12)

No.	Name	Count	Type	Full Name
1	ACY	6	Ligand/Ion	ACETIC ACID
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	VO4	2	Ligand/Ion	VANADATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:233 , SER A:238 , LYS A:240 , THR A:241 , LEU A:417	BINDING SITE FOR RESIDUE VO4 A 589
02	AC2	SOFTWARE	PRO A:233 , LEU A:417	BINDING SITE FOR RESIDUE VO4 A 590
03	AC3	SOFTWARE	ALA A:391	BINDING SITE FOR RESIDUE ACY A 591
04	AC4	SOFTWARE	GLU A:183 , ILE A:184 , LEU A:550 , LEU A:582 , HOH A:644	BINDING SITE FOR RESIDUE MPD A 592
05	AC5	SOFTWARE	THR A:241 , VAL A:242 , THR A:243 , PHE A:427 , PRO A:428 , ALA A:429	BINDING SITE FOR RESIDUE ACY A 593
06	AC6	SOFTWARE	GLN A:246 , LYS A:249 , ALA A:507	BINDING SITE FOR RESIDUE MPD A 594
07	AC7	SOFTWARE	ALA A:337 , PRO A:402 , VAL A:403 , ASN A:406	BINDING SITE FOR RESIDUE MPD A 595
08	AC8	SOFTWARE	ASN A:431 , TRP A:432 , LEU A:433 , HOH A:664	BINDING SITE FOR RESIDUE ACY A 596
09	AC9	SOFTWARE	LYS A:461 , ASP A:532	BINDING SITE FOR RESIDUE ACY A 597
10	BC1	SOFTWARE	TRP A:250 , GLU A:510 , VAL A:511 , TYR A:514 , ARG A:563 , HOH A:640	BINDING SITE FOR RESIDUE TRS A 598
11	BC2	SOFTWARE	GLY A:323 , ASP A:325 , VAL A:383	BINDING SITE FOR RESIDUE ACY A 599
12	BC3	SOFTWARE	ASN A:539 , ARG A:553 , GLU A:554	BINDING SITE FOR RESIDUE ACY A 600

(no "SS Bond" information available for 3P20)

(no "Cis Peptide Bond" information available for 3P20)

(no "SAP(SNP)/Variant" information available for 3P20)

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 3P20)

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:517
 aligned with VATA_PYRHO | O57728 from UniProtKB/Swiss-Prot  Length:964

    Alignment length:903
                                    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       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961   
           VATA_PYRHO    62 GEPVVGTGASLSVELGPGLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSGKCVDGDTLVLTKEFGLIKIKELYEKLDGKGRKIVEGNEEWTELEKPITVYGYKDGKIVEIKATHVYKGVSSGMVEIRTRTGRKIKVTPIHRLFTGRVTKDGLILKEVMAMHVKPGDRIAVVKKIDGGEYIKLDSSNVGEIKVPEILNEELAEFLGYLMANGTLKSGIIEIYCDDESLLERVNSLSLKLFGVGGRIVQKVDGKALVIQSKPLVDVLRRLGVPEDKKVENWKVPRELLLSPSNVVRAFVNAYIKGKEEVEITLASEEGAYELSYLFAKLGIYVTISKSGEYYKVRVSRRGNLDTIPVEVNGMPKVLPYEDFRKFAKSIGLEEVAENHLQHIIFDEVIDVRYIPEPQEVYDVTTETHNFVGGNMPTLLHNTVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 964
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                                                                                                                                                                                                                                                                                                                                                                                        ATP-synt_ab-3p20A01 A:241-437                                                                                                                                                                        ------------------ATP-synt_ab_C-3p20A03 A:456-588                                                                                                       Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                                                                                                                                                                                                                                                                                                                                                                                        ATP-synt_ab-3p20A02 A:241-437                                                                                                                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...........eeee.......ee...............................eeeeee......ee....eeeeee.....eeeee......eeeeee...eeee.....eeee.....eeee...eeee........ee..........hhhhhhhh......eeeee.......----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.hhhhhhhhhh...eeeeee........hhhhhh...........hhhh.eeeee.....hhhhhhhhhhhhhhhhhhhhhh..eeeeee................----------.hhhhhhhhhhhh..eeee.......eeeeeeeeee........hhhhhhhhh...ee...hhhhhhh...........ee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p20 A  62 GEPVVGTGASLSVELGPRLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSGK----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREISGR----------PAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 588
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        |-         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -     | 245       255       265       275       285       295       305       315       325       335       345|        - |     365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585   
                                                                                                                                                                                                            240                                                                                                                                                                                                                                                                                                                                                                                      241                                                                                                      346        357

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 3P20)

(no "CATH Domain" information available for 3P20)

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
(no "Cis Peptide Bonds" information available for 3p20)

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	VATA_PYRHO \| O57728
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	3.6.3.14
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	VATA_PYRHO \| O57728
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	VATA_PYRHO \| O57728	:	1vdz 3i4l 3i72 3i73 3ikj 3m4y 3mfy 3nd8 3nd9 3qg1 3qia 3qjy 3sdz 3se0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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Pfam Domains (2, 3)

Gene Ontology (16, 16)

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