2VWB - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE ARCHAEAL KAE1-BUD32 FUSION PROTEIN MJ1130: A MODEL FOR THE EUKARYOTIC EKC-KEOPS SUBCOMPLEX INVOLVED IN TRANSCRIPTION AND TELOMERE HOMEOSTASIS.

Authors :   A. Hecker, R. Lopreiato, M. Graille, B. Collinet, P. Forterre, D. Libri H. Van Tilbeurgh

Date :   20 Jun 08 (Deposition) - 19 Aug 08 (Release) - 27 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.05

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

Keywords :   Hydrolase, Ekc, Kae1, Bud32, Keops, Mj1130, Protease, Telomere, Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Hecker, R. Lopreiato, M. Graille, B. Collinet, P. Forterre, D. Libri, H. Van Tilbeurgh
Structure Of The Archaeal Kae1/Bud32 Fusion Protein Mj1130: A Model For The Eukaryotic Ekc/Keops Subcomplex
Embo J. V. 27 2340 2008
PubMed-ID: 19172740 | Reference-DOI: 10.1038/EMBOJ.2008.157

Molecule 1 - PUTATIVE O-SIALOGLYCOPROTEIN ENDOPEPTIDASE
	Chains	:	A, B
	EC Number	:	3.4.24.57
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-9A
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA PLYSS
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	243232
	Strain	:	DSM 2661
	Synonym	:	GLYCOPROTEASE, MJ1130

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ANP	2	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ANP	1	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:12 , HIS A:106 , HIS A:110 , TYR A:127 , SER A:129 , GLY A:130 , GLY A:131 , GLY A:155 , LEU A:158 , ASP A:159 , GLY A:172 , PRO A:173 , GLU A:176 , GLY A:252 , VAL A:253 , ASN A:256 , ASP A:284	BINDING SITE FOR RESIDUE ANP A1531
2	AC2	SOFTWARE	ALA B:10 , LYS B:12 , HIS B:106 , HIS B:110 , TYR B:127 , SER B:129 , GLY B:130 , GLY B:131 , GLY B:155 , LEU B:158 , ASP B:159 , PRO B:170 , GLY B:172 , PRO B:173 , GLU B:176 , GLY B:252 , VAL B:253 , ALA B:255 , ASN B:256 , GLY B:283 , ASP B:284	BINDING SITE FOR RESIDUE ANP B1533

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

Asymmetric Unit

No.	Residues
1	Gly A:76	-	Pro A:77
2	Gly B:76	-	Pro B:77

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOPROTEASE	PS01016	Glycoprotease family signature.	KAE1B_METJA	91-111	2	A:91-111 B:91-111
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	KAE1B_METJA	447-459	2	A:447-459 B:447-459

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOPROTEASE	PS01016	Glycoprotease family signature.	KAE1B_METJA	91-111	1	A:91-111 -
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	KAE1B_METJA	447-459	1	A:447-459 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOPROTEASE	PS01016	Glycoprotease family signature.	KAE1B_METJA	91-111	1	- B:91-111
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	KAE1B_METJA	447-459	1	- B:447-459

(no "Exon" information available for 2VWB)

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:519
 aligned with KAE1B_METJA | Q58530 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:530
                                    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
          KAE1B_METJA     1 MICLGLEGTAEKTGVGIVTSDGEVLFNKTIMYKPPKQGINPREAADHHAETFPKLIKEAFEVVDKNEIDLIAFSQGPGLGPSLRVTATVARTLSLTLKKPIIGVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLDQFARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAYDAGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLKAMCEGQNVDFYVPPKEFCGDNGAMIAWLGLLMHKNGRWMSLDETKIIPNYRTDMVEVNWIKEIKGKKRKIPEHLIGKGAEADIKRDSYLDFDVIIKERVKKGYRDERLDENIRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKLAKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISNLDEDKAVDLIVFKKAVLSTHHEKFDEIWERFLEGYKSVYDRWEIILELMKDVERR 530
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....eeeeeee.-----------..hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhh....eeeee....eeeeeee..eeeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh...........ee..ee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhh...eee..hhhhh..hhhhhhhhhhhhhhh....hhhhh....................................eeeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee....eeeee....eehhhhhh..hhhhhhhhhhhhhhhhh.ee........eee...eee......ee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------GLYCOPROTEASE        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vwb A   1 MICLGLEGTAEKTGVGIVTSDGEVLFNKTIM-----------EAADHHAETFPKLIKEAFEVVDKNEIDLIAFSQGPGLGPSLRVTATVARTLSLTLKKPIIGVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLDQFARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAYDAGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLKAMCEGQNVDFYVPPKEFCGDNGAMIAWLGLLMHKNGRWMSLDETKIIPNYRTDMVEVNWIKEIKGKKRKIPEHLIGKGAEADIKRDSYLDFDVIIKERVKKGYRDERLDENIRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKLAKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISNLDEDKAVDLIVFKKAVLSTHHEKFDEIWERFLEGYKSVYDRWEIILELMKDVERR 530
                                    10        20        30|        -  |     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
                                                         31          43

Chain B from PDB  Type:PROTEIN  Length:507
 aligned with KAE1B_METJA | Q58530 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:532
                                    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  
          KAE1B_METJA     1 MICLGLEGTAEKTGVGIVTSDGEVLFNKTIMYKPPKQGINPREAADHHAETFPKLIKEAFEVVDKNEIDLIAFSQGPGLGPSLRVTATVARTLSLTLKKPIIGVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLDQFARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAYDAGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLKAMCEGQNVDFYVPPKEFCGDNGAMIAWLGLLMHKNGRWMSLDETKIIPNYRTDMVEVNWIKEIKGKKRKIPEHLIGKGAEADIKRDSYLDFDVIIKERVKKGYRDERLDENIRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKLAKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISNLDEDKAVDLIVFKKAVLSTHHEKFDEIWERFLEGYKSVYDRWEIILELMKDVERRAR 532
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------Peptidase           _M22-2vwbB01 B:23-291                                                                                                                                                                                                                                    ----------------------------------              Pkinase-2vwbB03 B:340-486                                                                                                                          ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------Peptidase           _M22-2vwbB02 B:23-291                                                                                                                                                                                                                                    ----------------------------------              Pkinase-2vwbB04 B:340-486                                                                                                                          ---------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee.....eeeeeee.........ee.-----------..hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhh......eeeee....eeeeee....eeeeee....hhhhhhhhhhhhh.....hhhhhhhhhh...........ee..ee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...eee..hhhhhh.hhhhhhhhhhhhhhh....hhhhhh.....hhhhh......--------------.....eeeeeeee..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhh.eeeee....eehhhhh...hhhhhhhhhhhhhhhhh.ee........eee...eee......ee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------GLYCOPROTEASE        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vwb B   1 MICLGLEGTAEKTGVGIVTSDGEVLFNKTIM-----------EAADHHAETFPKLIKEAFEVVDKNEIDLIAFSQGPGLGPSLRVTATVARTLSLTLKKPIIGVNHCIAHIEIGKLTTEAEDPLTLYVSGGNTQVIAYVSKKYRVFGETLDIAVGNCLDQFARYVNLPHPGGPYIEELARKGKKLVDLPYTVKGMDIAFSGLLTAAMRAYDAGERLEDICYSLQEYAFSMLTEITERALAHTNKGEVMLVGGVAANNRLREMLKAMCEGQNVDFYVPPKEFCGDNGAMIAWLGLLMHKNGRWMSLDETKIIPNYRTDMVEVNWIK--------------GKGAEADIKRDSYLDFDVIIKERVKKGYRDERLDENIRKSRTAREARYLALVKDFGIPAPYIFDVDLDNKRIMMSYINGKLAKDVIEDNLDIAYKIGEIVGKLHKNDVIHNDLTTSNFIFDKDLYIIDFGLGKISNLDEDKAVDLIVFKKAVLSTHHEKFDEIWERFLEGYKSVYDRWEIILELMKDVERRAR 532
                                    10        20        30|        -  |     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    |    -       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530  
                                                         31          43                                                                                                                                                                                                                                                                                       325            340

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 2VWB)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (KAE1B_METJA | Q58530)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0061711	N(6)-L-threonylcarbamoyladenine synthase	Catalysis of the reaction: L-threonylcarbamoyladenylate + adenine(37) in tRNA = AMP + N(6)-L-threonylcarbamoyladenine(37) in tRNA.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0004672	protein kinase activity	Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0004712	protein serine/threonine/tyrosine kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
	GO:0016747	transferase activity, transferring acyl groups other than amino-acyl groups	Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	GO:0002949	tRNA threonylcarbamoyladenosine modification	The attachment of a carbonyl group and a threonine to the amino group of the adenine residue immediately 3' of the anticodon, in tRNAs that decode ANN codons (where N is any base).
cellular component
	GO:0000408	EKC/KEOPS complex	A protein complex involved in t6A tRNA modification; originally proposed to be involved in transcription as well as promoting telomere uncapping and telomere elongation. For example, in Saccharomyces cerevisiae the complex contains Bud32p, Kae1p, Gon7p, Cgi121p, and Pcc1p.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:76 - Pro A:77	[ RasMol ]
		Gly B:76 - Pro B:77	[ RasMol ]

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	2vwb
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	KAE1B_METJA \| Q58530
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	3.4.24.57
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	KAE1B_METJA \| Q58530	:	3en9 3enh 5jmv

(no "Related Entries Specified in the PDB File" available for 2VWB)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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