1M74 - JenaLib

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Title :   CRYSTAL STRUCTURE OF MG-ADP-BOUND SECA FROM BACILLUS SUBTILIS

Authors :   J. F. Hunt, S. Weinkauf, L. Henry, J. J. Fak, P. Mcnicholas, D. B. Oliver, J. Deisenhofer

Date :   16 Jul 02 (Deposition) - 20 Sep 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Protein Translocation; Atpase; Transmembrane Transport; Helicase Family Structure; Mechanochemisty, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. F. Hunt, S. Weinkauf, L. Henry, J. J. Fak, P. Mcnicholas, D. B. Oliver J. Deisenhofer
Nucleotide Control Of Interdomain Interactions In The Conformational Reaction Cycle Of Seca
Science V. 297 2018 2002
PubMed-ID: 12242434 | Reference-DOI: 10.1126/SCIENCE.1074424
(for further references see the PDB file header)

Molecule 1 - PREPROTEIN TRANSLOCASE SECA
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PT7-DIV
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET
	Gene	:	DIV
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	SECA

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:107 , ASP A:207 , ADP A:901 , HOH A:1146 , HOH A:1147	BINDING SITE FOR RESIDUE MG A 902
2	AC2	SOFTWARE	THR A:58 , THR A:120 , LYS A:122 , HIS A:202 , HOH A:1101	BINDING SITE FOR RESIDUE SO4 A 1003
3	AC3	SOFTWARE	ASN A:130 , GLU A:131 , HIS A:464	BINDING SITE FOR RESIDUE SO4 A 1004
4	AC4	SOFTWARE	LEU A:596 , ARG A:735 , GLN A:736	BINDING SITE FOR RESIDUE SO4 A 1005
5	AC5	SOFTWARE	TYR A:408 , ARG A:409 , THR A:410 , THR A:567	BINDING SITE FOR RESIDUE SO4 A 1006
6	AC6	SOFTWARE	GLU A:216 , ARG A:218 , THR A:219 , GLN A:798 , PRO A:799	BINDING SITE FOR RESIDUE SO4 A 1007
7	AC7	SOFTWARE	MET A:79 , PHE A:80 , PRO A:81 , PHE A:82 , GLN A:85 , GLY A:103 , GLU A:104 , GLY A:105 , LYS A:106 , THR A:107 , LEU A:108 , GLY A:490 , ASP A:492 , ARG A:528 , MG A:902 , HOH A:1146 , HOH A:1147	BINDING SITE FOR RESIDUE ADP A 901

(no "SS Bond" information available for 1M74)

(no "Cis Peptide Bond" information available for 1M74)

(no "SAP(SNP)/Variant" information available for 1M74)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SECA_MOTOR_DEAD	PS51196	SecA family profile.	SECA_BACSU	1-570	1	A:1-570
2	SECA	PS01312	SecA family signature.	SECA_BACSU	480-495	1	A:480-495

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SECA_MOTOR_DEAD	PS51196	SecA family profile.	SECA_BACSU	1-570	2	A:1-570
2	SECA	PS01312	SecA family signature.	SECA_BACSU	480-495	2	A:480-495

(no "Exon" information available for 1M74)

Asymmetric 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:802
 aligned with SECA_BACSU | P28366 from UniProtKB/Swiss-Prot  Length:841

    Alignment length:802
                                    10        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       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  
           SECA_BACSU     1 MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEIENNLEREEVVQGQTTAHQPQEG 802
               SCOP domains d1m74a3 A:1-226,A:349-395 Translocation ATPase SecA, nucleotide-binding domains                                                                                                                                                   d1m74a1 A:227-348 Pre-protein crosslinking domain of SecA                                                                 d1m74a3 A:1-226,A:349-395                      d1m74a4 A:396-570 Translocation ATPase SecA, nucleotide-binding domains                                                                                                        d1m74a2 A:571-802 Helical scaffold and wing domains of SecA                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----SecA_DEAD-1m74A02 A:5-382                                                                                                                                                                                                                                                                                                                                                                 ----------------------------------------------------------------Helicase_C-1m74A01 A:447-530                                                        -------------------------------------SecA_SW-1m74A04 A:568-780                                                                                                                                                                                            ---------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SecA_PP_bind-1m74A03 A:226-338                                                                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh.eeeeehhhhhhhhhhh....hhhhh......eeeeehhhhhhhhhhh..eeeee.....hhhhhhhhhhhh.......ee......ee..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.......eeee..eeee.............hhhhhhhhhhhhh........eeeeeehhhhhhh...eeeeee..hhhhhhhhhhhh...eee.........ee...eee.hhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh....eee...hhhhhhhhhhh......eeeee.............hhhhhh...eee.....hhhhhhhhhhh........eeeeeee....hhhhh.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) SECA_MOTOR_DEAD  PDB: A:1-570 UniProt: 1-570                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SECA            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m74 A   1 MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEIENNLEREEVVQGQTTAHQPQEG 802
                                    10        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       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

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 "CATH Domain" information available for 1M74)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Helicase_C (51)

Bacillus subtilis (6)

Helicase_C-1m74A01

A:447-530

Family: SecA_DEAD (9)

Bacillus subtilis (5)

SecA_DEAD-1m74A02

A:5-382

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

Family: SecA_PP_bind (9)

Bacillus subtilis (5)

SecA_PP_bind-1m74A03

A:226-338

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

Family: SecA_SW (9)

Bacillus subtilis (5)

SecA_SW-1m74A04

A:568-780

Asymmetric Unit(hide GO term definitions)

Chain A (SECA_BACSU | P28366)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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 Unit
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(no "Cis Peptide Bonds" information available for 1m74)

Biological Unit
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	1m74
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	SECA_BACSU \| P28366	:	1m6n 1tf2 1tf5 2ibm 3dl8 3iqm 3iqy 3jv2 5eul

1m6n	CRYSTAL STRUCTURE OF NUCLEOTIDE-FREE B. SUBTILIS SECA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

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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