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Title :   STRUCTURE OF THE TRANSLOCATION ATPASE SECA FROM THERMOTOGA MARITIMA

Authors :   J. Zimmer

Date :   15 Sep 09 (Deposition) - 20 Oct 09 (Release) - 12 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A

Keywords :   Protein Translocation, Atpase, Conformational Change, Peptide Binding, Atp-Binding, Cell Inner Membrane, Cell Membrane, Cytoplasm, Membrane, Nucleotide-Binding, Protein Transport, Translocation, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Zimmer, T. A. Rapoport
Conformational Flexibility And Peptide Interaction Of The Translocation Atpase Seca.
J. Mol. Biol. V. 394 606 2009
PubMed-ID: 19850053 | Reference-DOI: 10.1016/J.JMB.2009.10.024
(for further references see the PDB file header)

Molecule 1 - PROTEIN TRANSLOCASE SUBUNIT SECA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	C43
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SECA, TM_1578
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Strain	:	DSM 3109

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:252 , HOH A:823 , HOH A:824 , ADP A:873	BINDING SITE FOR RESIDUE MG A 872
2	AC2	SOFTWARE	PHE A:77 , GLN A:80 , LYS A:96 , GLY A:98 , GLU A:99 , GLY A:100 , LYS A:101 , THR A:102 , LEU A:103 , TRP A:135 , GLY A:535 , ASP A:537 , LYS A:539 , HOH A:823 , HOH A:824 , MG A:872	BINDING SITE FOR RESIDUE ADP A 873

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

Asymmetric/Biological Unit

No.	Residues
1	Ser A:152	-	Leu A:153
2	Lys A:300	-	Ala A:301
3	Ala A:301	-	Arg A:302
4	Ile A:318	-	Gly A:319
5	Val A:349	-	Asp A:350
6	Val A:361	-	Asp A:362
7	Thr A:365	-	Gly A:366
8	Pro A:370	-	Gly A:371
9	Val A:388	-	Pro A:389
10	Ile A:608	-	Glu A:609
11	Ala A:707	-	Gly A:708
12	Tyr A:781	-	Gly A:782
13	Gly A:782	-	Gln A:783

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SECA	PS01312	SecA family signature.	SECA_THEMA	525-540	1	A:525-540

(no "Exon" information available for 3JUX)

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:813
 aligned with SECA_THEMA | Q9X1R4 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:813
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813   
           SECA_THEMA     4 FDKNKRILKKYAKMVSKINQIESDLRSKKNSELIRLSMVLKEKVNSFEDADEHLFEAFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEGKTLAATMPIYLNALIGKGVHLVTVNDYLARRDALWMGPVYLFLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGKVMNILKIEEGQPIQHPMLSKLIENIQKKVEGINFSIRKTLMEMDDVLDKQRRAVYSLRDQILLEKDYDEYLKDIFEDVVSTRVEEFCSGKNWDIESLKNSLSFFPAGLFDLDEKQFSSSEELHDYLFNRLWEEYQRKKQEIGEDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV 816
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) SecA_DEAD-3juxA02 A:4-427                                                                                                                                                                                                                                                                                                                                                                                                               ----------------------------------------------------------------Helicase_C-3juxA01 A:492-575                                                        -------------------------------------SecA_SW-3juxA04 A:613-816                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SecA_PP_bind-3juxA03 A:271-383                                                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhh...eeeee...eeeeeee.hhhhhhhhhhh..............hhhhh.hhhhhhh.eeeee.hhhhhhhh.eeeeehhhhhhhhhhhh..............eeeeehhhhhhhhhhhh.eeee.....hhhhhhhhhhhh........eee......eeehhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....eeee..eeee................hhhhhhhhhhh........eeeeehhhhhhh...eeeeee.....hhhhhhhhh...eee.........eee.eeee.hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhhhh...eeeee.....................eeee.....hhhhhhhhhh.........eeeeeee.........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh......hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SECA            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jux A   4 FDKNKRILKKYAKMVSKINQIESDLRSKKNSELIRLSMVLKEKVNSFEDADEHLFEAFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEGKTLAATMPIYLNALIGKGVHLVTVNDYLARRDALWMGPVYLFLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGKVMNILKIEEGQPIQHPMLSKLIENIQKKVEGINFSIRKTLMEMDDVLDKQRRAVYSLRDQILLEKDYDEYLKDIFEDVVSTRVEEFCSGKNWDIESLKNSLSFFPAGLFDLDEKQFSSSEELHDYLFNRLWEEYQRKKQEIGEDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRV 816
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813

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 3JUX)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Helicase_C (51)

Thermotoga maritima (1)

Helicase_C-3juxA01

A:492-575

Family: SecA_DEAD (9)

Thermotoga maritima (1)

SecA_DEAD-3juxA02

A:4-427

Clan: no clan defined [family: SecA_PP_bind] (9)

Family: SecA_PP_bind (9)

Thermotoga maritima (1)

SecA_PP_bind-3juxA03

A:271-383

Clan: no clan defined [family: SecA_SW] (9)

Family: SecA_SW (9)

Thermotoga maritima (1)

SecA_SW-3juxA04

A:613-816

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SECA_THEMA | Q9X1R4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0065002	intracellular protein transmembrane transport	The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0017038	protein import	The targeting and directed movement of proteins into a cell or organelle. Not all import involves an initial targeting event.
	GO:0006605	protein targeting	The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
	GO:0015031	protein transport	The directed movement of proteins 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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:301 - Arg A:302	[ RasMol ]
		Ala A:707 - Gly A:708	[ RasMol ]
		Gly A:782 - Gln A:783	[ RasMol ]
		Ile A:318 - Gly A:319	[ RasMol ]
		Ile A:608 - Glu A:609	[ RasMol ]
		Lys A:300 - Ala A:301	[ RasMol ]
		Pro A:370 - Gly A:371	[ RasMol ]
		Ser A:152 - Leu A:153	[ RasMol ]
		Thr A:365 - Gly A:366	[ RasMol ]
		Tyr A:781 - Gly A:782	[ RasMol ]
		Val A:349 - Asp A:350	[ RasMol ]
		Val A:361 - Asp A:362	[ RasMol ]
		Val A:388 - Pro A:389	[ RasMol ]

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	3jux
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(no "Related Entries Specified in the PDB File" available for 3JUX)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (13, 13)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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