2R62 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HELICOBACTER PYLORI ATP DEPENDENT PROTEASE, FTSH

Authors :   S. H. Kim, G. B. Kang, H. -E. Song, S. J. Park, M. -H. Bae, S. H. Eom

Date :   05 Sep 07 (Deposition) - 09 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

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

Keywords :   Ftsh, Atpase Domain, Helicobacter Pylori, Atp-Binding, Cell Cycle, Cell Division, Hydrolase, Membrane, Metal-Binding, Metalloprotease, Nucleotide-Binding, Protease, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Kim, G. B. Kang, H. -E. Song, S. J. Park, M. -H. Bea, S. H. Eom
Structural Studies On Helicobacter Pyloriatp-Dependent Protease, Ftsh
J. Synchrotron Radiat. V. 15 208 2008
PubMed-ID: 18421140 | Reference-DOI: 10.1107/S090904950706846X

Molecule 1 - CELL DIVISION PROTEASE FTSH HOMOLOG
	Chains	:	A, B
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	ATPASE DOMAIN, UNP RESIDUES 160-419
	Gene	:	FTSH
	Mutation	:	YES
	Organism Common	:	CAMPYLOBACTER PYLORI
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2R62)

(no "Site" information available for 2R62)

(no "SS Bond" information available for 2R62)

Asymmetric Unit

No.	Residues
1	Ala A:262	-	Pro A:263
2	Ala B:262	-	Pro B:263

(no "SAP(SNP)/Variant" information available for 2R62)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AAA	PS00674	AAA-protein family signature.	FTSH_HELPY	311-329	2	A:311-329 B:311-329

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AAA	PS00674	AAA-protein family signature.	FTSH_HELPY	311-329	1	A:311-329 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AAA	PS00674	AAA-protein family signature.	FTSH_HELPY	311-329	1	- B:311-329

(no "Exon" information available for 2R62)

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:249
 aligned with FTSH_HELPY | P71408 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:259
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409         
           FTSH_HELPY   160 INAEKPNVRFNDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhh............................hhhhhhhh...eeee.hhhhh..----------.........................eeee........hhhhhh................hhhhhhhhhh.....................hhhhhhhhhhhhhhh.........hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: A:311-329----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r62 A 160 INAEKPNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGK----------NDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
                                   169       179       189       199       209       219       229       239       249       259       269      |  -       289       299       309       319       329       339       349       359       369       379       389       399       409         
                                                                                                                                              276        287

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with FTSH_HELPY | P71408 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:259
                                   169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409         
           FTSH_HELPY   160 INAEKPNVRFNDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------AAA-2r62B01 B:206-341                                                                                                                   -----------------------------------------------------------Peptidase_M41-2r62 Pfam domains (1)
           Pfam domains (2) ----------------------------------------------AAA-2r62B02 B:206-341                                                                                                                   -----------------------------------------------------------Peptidase_M41-2r62 Pfam domains (2)
         Sec.struct. author ................hhhhhhhhhhhhhhhh...hhhhh.....eeeee.....hhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh...eee.hhhhhh.----------.........hhhhhh...........eeeee.hhhhh......................hhhhh.hhhhh...........hhhhhh.....hhhhhhhhhhhhhh............hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: B:311-329----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r62 B 160 INAEKPNVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGK----------NDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQHLKEAVERGIAGLEK 418
                                   169       179       189       199       209       219       229       239       249       259       269      |  -       289       299       309       319       329       339       349       359       369       379       389       399       409         
                                                                                                                                              276        287

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 2R62)

(no "CATH Domain" information available for 2R62)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AAA (26)

Helicobacter pylori (Campylobacter pylori) (2)

1a	AAA-2r62B01	B:206-341
1b	AAA-2r62B02	B:206-341

Clan: Peptidase_MA (251)

Family: Peptidase_M41 (5)

Helicobacter pylori (Campylobacter pylori) (2)

2a	Peptidase_M41-2r62B03	B:401-418
2b	Peptidase_M41-2r62B04	B:401-418

Asymmetric Unit(hide GO term definitions)

Chain A,B (FTSH_HELPY | P71408)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	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.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0030163	protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2r62)

	Sites
(no "Sites" information available for 2r62)

	Cis Peptide Bonds
		Ala A:262 - Pro A:263	[ RasMol ]
		Ala B:262 - Pro B:263	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2r62
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
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Access by UniProt ID/Accession number
	FTSH_HELPY \| P71408
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.4.24.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	FTSH_HELPY \| P71408
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UniProtKB/Swiss-Prot
	FTSH_HELPY \| P71408	:	2r65

2r65	THE SAME PROTEIN IN COMPLEX WITH ADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (14, 14)

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Related Entries

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