3H4M - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   AAA ATPASE DOMAIN OF THE PROTEASOME- ACTIVATING NUCLEOTIDASE

Authors :   P. Jeffrey, F. Zhang, M. Hu, G. Tian, P. Zhang, D. Finley, Y. Shi

Date :   20 Apr 09 (Deposition) - 09 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.11

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Atpase, Proteasome, Pan, Atp-Binding, Nucleotide-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Zhang, M. Hu, G. Tian, P. Zhang, D. Finley, P. D. Jeffrey, Y. Shi
Structural Insights Into The Regulatory Particle Of The Proteasome From Methanocaldococcus Jannaschii.
Mol. Cell V. 34 473 2009
PubMed-ID: 19481527 | Reference-DOI: 10.1016/J.MOLCEL.2009.04.021

Molecule 1 - PROTEASOME-ACTIVATING NUCLEOTIDASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Fragment	:	PAN ATPASE DOMAIN (155-430)
	Gene	:	PAN, MJ1176
	Organism Common	:	METHANOCOCCUS JANNASCHII
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	PROTEASOME REGULATORY SUBUNIT

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:171 , ILE A:172 , GLY A:173 , PRO A:213 , GLY A:214 , THR A:215 , GLY A:216 , LYS A:217 , THR A:218 , LEU A:219 , HIS A:353 , GLY A:377 , ALA A:378	BINDING SITE FOR RESIDUE ADP A 439
2	AC2	SOFTWARE	ASP B:171 , ILE B:172 , GLY B:173 , LEU B:175 , PRO B:213 , GLY B:214 , THR B:215 , GLY B:216 , LYS B:217 , THR B:218 , LEU B:219 , HIS B:353 , GLY B:377 , ALA B:378	BINDING SITE FOR RESIDUE ADP B 439
3	AC3	SOFTWARE	ASP C:171 , GLY C:173 , GLY C:214 , THR C:215 , GLY C:216 , LYS C:217 , THR C:218 , HIS C:353 , GLY C:377 , ALA C:378 , LYS C:381	BINDING SITE FOR RESIDUE ADP C 439

(no "SS Bond" information available for 3H4M)

Asymmetric Unit

No.	Residues
1	Ala A:263	-	Pro A:264
2	Ala B:263	-	Pro B:264
3	Ala C:263	-	Pro C:264

(no "SAP(SNP)/Variant" information available for 3H4M)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AAA	PS00674	AAA-protein family signature.	PAN_METJA	310-328	3	A:310-328 B:310-328 C:310-328

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AAA	PS00674	AAA-protein family signature.	PAN_METJA	310-328	1	A:310-328 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AAA	PS00674	AAA-protein family signature.	PAN_METJA	310-328	1	- B:310-328 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AAA	PS00674	AAA-protein family signature.	PAN_METJA	310-328	1	- - C:310-328

(no "Exon" information available for 3H4M)

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:261
 aligned with PAN_METJA | Q58576 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:261
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417 
            PAN_METJA   158 AMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIMEKKKVK 418
               SCOP domains d3h4ma_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhh..eeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh........hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: A:310-328------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h4m A 158 AMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIMEKKKVK 418
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with PAN_METJA | Q58576 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:261
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417 
            PAN_METJA   158 AMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIMEKKKVK 418
               SCOP domains d3h4mb_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhh..eeeeee.hhh.....hhhhhhhhhhhhhhhhh..eeeeeehhhhh...........hhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhh....eeeeee....hhhhhhhhhhhhhh........hhhhhhhhh...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: B:310-328------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h4m B 158 AMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIMEKKKVK 418
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417

Chain C from PDB  Type:PROTEIN  Length:261
 aligned with PAN_METJA | Q58576 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:261
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417 
            PAN_METJA   158 AMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIMEKKKVK 418
               SCOP domains d3h4mc_ C: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhh..hhhhhhhhhh..hhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhh..eeeeee.hhh........hhhhhhhhhhhhhh..eeeeeehhhhh...........hhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhh...eeeeee....hhhhhhhhhhhh..........hhhhhhh.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------AAA  PDB: C:310-328------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h4m C 158 AMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTMDDFRKAVEKIMEKKKVK 418
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: automated matches (303)

Protein domain: automated matches (303)

Methanocaldococcus jannaschii [TaxId: 2190] (5)

1a	d3h4ma_	A:
1b	d3h4mc_	C:
1c	d3h4mb_	B:

(no "CATH Domain" information available for 3H4M)

(no "Pfam Domain" information available for 3H4M)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PAN_METJA | Q58576)

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:0043273	CTPase activity	Catalysis of the reaction: CTP + H2O = CDP + phosphate. May or may not be coupled to another reaction.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0017025	TBP-class protein binding	Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
	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:0036402	proteasome-activating ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate, which promotes unfolding of protein substrates, and channel opening of the core proteasome.
biological process
	GO:0045899	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly	Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
	GO:1901800	positive regulation of proteasomal protein catabolic process	Any process that activates or increases the frequency, rate or extent of proteasomal protein catabolic process.
	GO:0010498	proteasomal protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
	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:0043335	protein unfolding	The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state.
	GO:0030433	ubiquitin-dependent ERAD pathway	The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031597	cytosolic proteasome complex	A proteasome complex found in the cytosol of a cell.
	GO:0031595	nuclear proteasome complex	A proteasome found in the nucleus of a cell.
	GO:0000502	proteasome complex	A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core.
	GO:0008540	proteasome regulatory particle, base subcomplex	The subcomplex of the proteasome regulatory particle that directly associates with the proteasome core complex.
	GO:0022623	proteasome-activating nucleotidase complex	A homohexameric complex that recognizes and unfolds core proteasome substrate proteins, and translocates them to the core complex in an ATP dependent manner.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:263 - Pro A:264	[ RasMol ]
		Ala B:263 - Pro B:264	[ RasMol ]
		Ala C:263 - Pro C:264	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
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		Biological Unit 3	[ Jena3D ]

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	3h4m
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	PAN_METJA \| Q58576
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	PAN_METJA \| Q58576	:	3h43 3ipm

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

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