1XHK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF M. JANNASCHII LON PROTEOLYTIC DOMAIN

Authors :   Y. J. Im, Y. Na, G. B. Kang, S. -H. Rho, M. -K. Kim, J. H. Lee, C. H. Chung, S. H. Eom

Date :   20 Sep 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Lon Protease, Protease La, Atp Dependent, Catalytic Dyad, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. J. Im, Y. Na, G. B. Kang, S. H. Rho, M. K. Kim, J. H. Lee, C. H. Chung, S. H. Eom
The Active Site Of A Lon Protease From Methanococcus Jannaschii Distinctly Differs From The Canonical Catalytic Dyad Of Lon Proteases.
J. Biol. Chem. V. 279 53451 2004
PubMed-ID: 15456757 | Reference-DOI: 10.1074/JBC.M410437200
(for further references see the PDB file header)

Molecule 1 - PUTATIVE PROTEASE LA HOMOLOG
	Chains	:	A, B
	EC Number	:	3.4.21.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	MJ1417
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH B:172 , HOH B:220 , LYS B:458 , LYS B:478	BINDING SITE FOR RESIDUE SO4 B 302
2	AC2	SOFTWARE	HOH B:87 , HOH B:105 , HOH B:190 , SER B:544 , LYS B:545	BINDING SITE FOR RESIDUE SO4 B 303
3	AC3	SOFTWARE	HOH A:82 , SER A:497 , GLY A:498	BINDING SITE FOR RESIDUE SO4 A 305
4	AC4	SOFTWARE	HOH B:267 , HIS B:454 , TYR B:463 , GLN B:570 , ASP B:571 , TYR B:600 , GLY B:601 , PHE B:602 , LYS B:603	BINDING SITE FOR RESIDUE MES B 301

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LON_PROTEOLYTIC	PS51786	Lon proteolytic domain profile.	LONB_METJA	456-639	2	A:456-639 B:456-639

(no "Exon" information available for 1XHK)

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:185
 aligned with LONB_METJA | Q58812 from UniProtKB/Swiss-Prot  Length:649

    Alignment length:185
                                   465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635     
           LONB_METJA   456 EPKVGVIYGLAVLGAGGIGDVTKIIVQILESKNPGTHLLNISGDIAKHSITLASALSKKLVAEKKLPLPKKDIDLNNKEIYIQFSQSYSKIDGDSATAAVCLAIISALLDIPLKQDFAITGSLDLSGNVLAIGGVNEKIEAAKRYGFKRVIIPEANMIDVIETEGIEIIPVKTLDEIVPLVFDLD 640
               SCOP domains d1xhka_ A: ATP-dependent protease Lon (La), catalytic domain                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee........eeeeeeeeeee....eeeee..hhhhhhhhhhhhhhhhhhhhhh..............eeeeeee.......hhhhhhhhhhhhhhhhhhh......eee..ee.....ee...hhhhhhhhhhhh...eeeee.hhhhhh......eeeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LON_PROTEOLYTIC  PDB: A:456-639 UniProt: 456-639                                                                                                                                        - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhk A 456 EPKVGVIYGLAVLGAGGIGDVTKIIVQILESKNPGTHLLNISGDIAKHSITLASALSKKLVAEKKLPLPKKDIDLNNKEIYIQFSQSYSKIDGDSATAAVCLAIISALLDIPLKQDFAITGSLDLSGNVLAIGGVNEKIEAAKRYGFKRVIIPEANmIDVIETEGIEIIPVKTLDEIVPLVFDLD 640
                                   465       475       485       495       505       515       525       535       545       555       565       575       585       595       605      |615       625       635     
                                                                                                                                                                                      612-MSE

Chain B from PDB  Type:PROTEIN  Length:187
 aligned with LONB_METJA | Q58812 from UniProtKB/Swiss-Prot  Length:649

    Alignment length:187
                                   463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       
           LONB_METJA   454 NDEPKVGVIYGLAVLGAGGIGDVTKIIVQILESKNPGTHLLNISGDIAKHSITLASALSKKLVAEKKLPLPKKDIDLNNKEIYIQFSQSYSKIDGDSATAAVCLAIISALLDIPLKQDFAITGSLDLSGNVLAIGGVNEKIEAAKRYGFKRVIIPEANMIDVIETEGIEIIPVKTLDEIVPLVFDLD 640
               SCOP domains d1xhkb_ B: ATP-dependent protease Lon (La), catalytic domain                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Lon_C-1xhkB01 B:456-638                                                                                                                                                                -- Pfam domains (1)
           Pfam domains (2) --Lon_C-1xhkB02 B:456-638                                                                                                                                                                -- Pfam domains (2)
         Sec.struct. author .......eeeeeeee....eeeeeeeeeeeee....eeeee..hhhhhhhhhhhhhhhhhhhhhh..............eeeeeee.......hhhhhhhhhhhhhhhhhh.......eee..ee.....ee...hhhhhhhhhhhh...eeeee.hhhhhh......eeeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --LON_PROTEOLYTIC  PDB: B:456-639 UniProt: 456-639                                                                                                                                        - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xhk B 454 HmEPKVGVIYGLAVLGAGGIGDVTKIIVQILESKNPGTHLLNISGDIAKHSITLASALSKKLVAEKKLPLPKKDIDLNNKEIYIQFSQSYSKIDGDSATAAVCLAIISALLDIPLKQDFAITGSLDLSGNVLAIGGVNEKIEAAKRYGFKRVIIPEANmIDVIETEGIEIIPVKTLDEIVPLVFDLD 640
                             |     463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       
                           455-MSE                                                                                                                                                      612-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ribosomal protein S5 domain 2-like (306)

Superfamily: Ribosomal protein S5 domain 2-like (306)

Family: ATP-dependent protease Lon (La), catalytic domain (3)

Protein domain: ATP-dependent protease Lon (La), catalytic domain (3)

Methanococcus jannaschii [TaxId: 2190] (1)

1a	d1xhka_	A:
1b	d1xhkb_	B:

(no "CATH Domain" information available for 1XHK)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: S5 (103)

Family: Lon_C (14)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth (1)

1a	Lon_C-1xhkB01	B:456-638
1b	Lon_C-1xhkB02	B:456-638

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LONB_METJA | Q58812)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004176	ATP-dependent peptidase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds.
	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: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:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xhk)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1xhk
		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
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LONB_METJA \| Q58812
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.21.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LONB_METJA \| Q58812
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1XHK)

(no "Related Entries Specified in the PDB File" available for 1XHK)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File