3ND8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

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

Authors :   A. Kumar, G. Gruber

Date :   07 Jun 10 (Deposition) - 30 Mar 11 (Release) - 11 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase (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 (UNP RESIDUES 1-240, 617-964)
	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, V-ATPASE SUBUNIT A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:246 , LYS A:249 , HOH A:807	BINDING SITE FOR RESIDUE MRD A 589
2	AC2	SOFTWARE	ASP A:420 , ASN A:431 , TRP A:432 , LEU A:433 , HOH A:653 , HOH A:717 , HOH A:773	BINDING SITE FOR RESIDUE MRD A 590
3	AC3	SOFTWARE	LYS A:198 , PRO A:200 , TYR A:201 , LYS A:202	BINDING SITE FOR RESIDUE MRD A 591
4	AC4	SOFTWARE	MET A:458 , LYS A:461 , LEU A:528 , ASP A:532 , HOH A:720 , HOH A:778	BINDING SITE FOR RESIDUE MPD A 592
5	AC5	SOFTWARE	ARG A:499 , GLU A:500 , GLN A:504 , HOH A:622 , HOH A:799	BINDING SITE FOR RESIDUE ACY A 593
6	AC6	SOFTWARE	ALA A:240 , THR A:241 , ALA A:419 , HOH A:874	BINDING SITE FOR RESIDUE SO4 A 594
7	AC7	SOFTWARE	GLU A:555 , GLU A:562 , LYS A:567 , HOH A:855	BINDING SITE FOR RESIDUE MRD A 595
8	AC8	SOFTWARE	ASP A:252 , TYR A:514 , PRO A:517 , HOH A:758 , HOH A:860	BINDING SITE FOR RESIDUE MPD A 596

(no "SS Bond" information available for 3ND8)

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 3ND8)

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 3ND8)

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:510
 aligned with VATA_PYRHO | O57728 from UniProtKB/Swiss-Prot  Length:964

    Alignment length:902
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962  
           VATA_PYRHO    63 EPVVGTGASLSVELGPGLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSGKCVDGDTLVLTKEFGLIKIKELYEKLDGKGRKIVEGNEEWTELEKPITVYGYKDGKIVEIKATHVYKGVSSGMVEIRTRTGRKIKVTPIHRLFTGRVTKDGLILKEVMAMHVKPGDRIAVVKKIDGGEYIKLDSSNVGEIKVPEILNEELAEFLGYLMANGTLKSGIIEIYCDDESLLERVNSLSLKLFGVGGRIVQKVDGKALVIQSKPLVDVLRRLGVPEDKKVENWKVPRELLLSPSNVVRAFVNAYIKGKEEVEITLASEEGAYELSYLFAKLGIYVTISKSGEYYKVRVSRRGNLDTIPVEVNGMPKVLPYEDFRKFAKSIGLEEVAENHLQHIIFDEVIDVRYIPEPQEVYDVTTETHNFVGGNMPTLLHNTVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 964
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                                                                                                                                                                                                                                                                                                                                                                                        -ATP-synt_ab-3nd8A01 A:241-437                                                                                                                                                                        ------------------ATP-synt_ab_C-3nd8A03 A:456-588                                                                                                       Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                                                                                                                                                                                                                                                                                                                                                                                        -ATP-synt_ab-3nd8A02 A:241-437                                                                                                                                                                        ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..........eeee.......ee................................eeeee......ee....eeeeee.....eeeee......eeeeee...eee......eeee.....eeee...eeee........eee.........hhhhhhhh......eeeee......----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------..hhhhhhhhhh...eeeeeeeee.hhhhhhhhhhh..........hhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeee..........----------------.hhhhhhhhhhhh..eeee.......eeeeeeeeee........hhhhhhhhhhh.eeeeehhhhhhh.....eeeeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------INTEIN_C_TER            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_ALP------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nd8 A  63 EPVVGTGASLSVELGPRLLTSIYDGIQRPLEVIREKTGDFIARGVTAPALPRDKKWHFIPKAKVGDKVVGGDIIGEVPETSIIVHKIMVPPGIEGEIVEIAEEGDYTIEEVIAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPLITGQRVIDTFFPQAKGGTAAIPGPFGSG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATVTQHQLAKWSDAQVVIYIGCGERGNEMTDVLEEFPKLKDPKTGKPLMERTVLIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADSTSRWAEAL----------------PAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAVSPPGGDFSEPVVQNTLRVVKVFWALDADLARRRHFPAINWLTSYSLYVDAVKDWWHKNIDPEWKAMRDKAMALLQKESELQEIVRIVGPDALPERERAILLVARMLREDYLQQDAFDEVDTYCPPEKQVTMMRVLLNFYDKTMEAINRGVPLEEIAKLPVREEIGRMKFERDVSKIRSLIDKTNEQFEELFKKYGA 588
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      |  -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -   |   246       256       266       276       286       296       306       316       326       336   |     -         -|      366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586  
                                                                                                                                                                                                          239                                                                                                                                                                                                                                                                                                                                                                                      240                                                                                                 340              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 3ND8)

(no "CATH Domain" information available for 3ND8)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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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