2ZHO - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE REGULATORY SUBUNIT OF ASPARTATE KINASE FROM THERMUS THERMOPHILUS (LIGAND FREE FORM)

Authors :   A. Yoshida, T. Tomita, T. Kuzuyama, M. Nishiyama

Date :   06 Feb 08 (Deposition) - 17 Feb 09 (Release) - 23 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.98

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

Keywords :   Regulatory Domain, Act Domain, Alternative Initiation, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Kinase, Lysine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Yoshida, T. Tomita, H. Kono, S. Fushinobu, T. Kuzuyama, M. Nishiyama
Crystal Structures Of The Regulatory Subunit Of Thr-Sensitive Aspartate Kinase From Thermus Thermophilus
Febs J. V. 276 3124 2009
PubMed-ID: 19490113 | Reference-DOI: 10.1111/J.1742-4658.2009.07030.X
(for further references see the PDB file header)

Molecule 1 - ASPARTOKINASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.7.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26B(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	REGULATORY SUBUNIT, ASPARTOKINASE SUBUNIT ALPHA AND BETA, UNP RESIDUES 245-405
	Gene	:	ASK
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Strain	:	AT-62
	Synonym	:	ASPARTATE KINASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2ZHO)

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

Asymmetric Unit

No.	Residues
1	Glu D:79	-	Pro D:80
2	Arg D:92	-	Pro D:93

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

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	AK_THETH	263-347	6	A:19-103 B:19-103 C:19-103 D:19-103 E:19-103 F:19-103

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	AK_THETH	263-347	2	A:19-103 B:19-103 - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	AK_THETH	263-347	2	- - C:19-103 D:19-103 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACT	PS51671	ACT domain profile.	AK_THETH	263-347	2	- - - - E:19-103 F:19-103

(no "Exon" information available for 2ZHO)

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:151
 aligned with AK_THETH | P61489 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:154
                                   257       267       277       287       297       307       317       327       337       347       357       367       377       387       397    
             AK_THETH   248 DKAVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGHDPSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 401
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeeeeeee...hhhhhhhhhh......eeeee....---..eee.eeeeehhhhhhhhhhhhhhhhhhh.eeeee..eeeeeeee......hhhhhhhhhhhhhh.....eeee...eeeeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------ACT  PDB: A:19-103 UniProt: 263-347                                                  ------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zho A   4 DKAVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVP---PSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 157
                                    13        23        33        43        53   |    63        73        83        93       103       113       123       133       143       153    
                                                                            53  57

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with AK_THETH | P61489 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:154
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398    
             AK_THETH   249 KAVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGHDPSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFEL 402
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeee......hhhhhhhhhhhh.......eee..-------.eeeeeee..hhhhhhhhhhhhhhhhh.eeeee..eeeeeeee......hhhhhhhhhhhhh......eeee...eeeeeee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------ACT  PDB: B:19-103 UniProt: 263-347                                                  ------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zho B   5 KAVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGV-------QQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFEL 158
                                    14        24        34        44       | -     |  64        74        84        94       104       114       124       134       144       154    
                                                                          52      60

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with AK_THETH | P61489 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:153
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398   
             AK_THETH   249 KAVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGHDPSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 401
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeeeee...hhhhhhhhhhhh.......eee....--..eeeeeeeee..hhhhhhhhhhhhhhhhh.eeeee..eeeeeeee......hhhhhhhhhhhhh......eeee...eeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------ACT  PDB: C:19-103 UniProt: 263-347                                                  ------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zho C   5 KAVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPG--PSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 157
                                    14        24        34        44        54  |     64        74        84        94       104       114       124       134       144       154   
                                                                            54 57

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with AK_THETH | P61489 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:152
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399  
             AK_THETH   250 AVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGHDPSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 401
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eee....ee...hhhhhhhhhhhhh.....eee....---..ee..eeeehhhhhhhhhhhh..hhhhhh..ee....eeeeeeee......hhhhhhhhhhhhh......eee....eeeeeee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------ACT  PDB: D:19-103 UniProt: 263-347                                                  ------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zho D   6 AVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVP---PSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 157
                                    15        25        35        45       | - |      65        75        85        95       105       115       125       135       145       155  
                                                                          53  57

Chain E from PDB  Type:PROTEIN  Length:150
 aligned with AK_THETH | P61489 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:152
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399  
             AK_THETH   250 AVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGHDPSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 401
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee......hhhhhhhhhhhhh......eee.....--...eeeeeee..hhhhhhhhhhhhhhhhh.eeeee..eeeeeeee......hhhhhhhhhhhhh......eeee....eeeeee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------ACT  PDB: E:19-103 UniProt: 263-347                                                  ------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zho E   6 AVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGH--SRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 157
                                    15        25        35        45        55  |     65        75        85        95       105       115       125       135       145       155  
                                                                            55 58

Chain F from PDB  Type:PROTEIN  Length:148
 aligned with AK_THETH | P61489 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:152
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399  
             AK_THETH   250 AVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGVPGHDPSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 401
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------ACT-2zhoF01 F:99-157                                        Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------ACT-2zhoF02 F:99-157                                        Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------ACT-2zhoF03 F:99-157                                        Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------ACT-2zhoF04 F:99-157                                        Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------ACT-2zhoF05 F:99-157                                        Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------ACT-2zhoF06 F:99-157                                        Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------ACT-2zhoF07 F:99-157                                        Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------ACT-2zhoF08 F:99-157                                        Pfam domains (8)
           Pfam domains (9) ---------------------------------------------------------------------------------------------ACT-2zhoF09 F:99-157                                        Pfam domains (9)
          Pfam domains (10) ---------------------------------------------------------------------------------------------ACT-2zhoF10 F:99-157                                        Pfam domains (10)
          Pfam domains (11) ---------------------------------------------------------------------------------------------ACT-2zhoF11 F:99-157                                        Pfam domains (11)
          Pfam domains (12) ---------------------------------------------------------------------------------------------ACT-2zhoF12 F:99-157                                        Pfam domains (12)
         Sec.struct. author .eeeeeee..eeeeeeeee....hhhhhhhhhhhhh......eee..----...eeeeeeee..hhhhhhhhhhhhhhhhh.eeeee..eeeeeeee......hhhhhhhhhhhhhh.....eeee...eeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------ACT  PDB: F:19-103 UniProt: 263-347                                                  ------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zho F   6 AVTGVALDLDHAQIGLIGIPDQPGIAAKVFQALAERGIAVDMIIQGV----PSRQQMAFTVKKDFAQEALEALEPVLAEIGGEAILRPDIAKVSIVGVGLASTPEVPAKMFQAVASTGANIEMIATSEVRISVIIPAEYAEAALRAVHQAFE 157
                                    15        25        35        45      |  - |      65        75        85        95       105       115       125       135       145       155  
                                                                         52   57

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 2ZHO)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ACT (34)

Family: ACT (19)

Thermus thermophilus (1)

1a	ACT-2zhoF01	F:99-157
1b	ACT-2zhoF02	F:99-157
1c	ACT-2zhoF03	F:99-157
1d	ACT-2zhoF04	F:99-157
1e	ACT-2zhoF05	F:99-157
1f	ACT-2zhoF06	F:99-157
1g	ACT-2zhoF07	F:99-157
1h	ACT-2zhoF08	F:99-157
1i	ACT-2zhoF09	F:99-157
1j	ACT-2zhoF10	F:99-157
1k	ACT-2zhoF11	F:99-157
1l	ACT-2zhoF12	F:99-157

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (AK_THETH | P61489)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0004072	aspartate kinase activity	Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019877	diaminopimelate biosynthetic process	The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0009089	lysine biosynthetic process via diaminopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
	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:0009088	threonine biosynthetic process	The chemical reactions and pathways resulting in the formation of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2zho)

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

	Cis Peptide Bonds
		Arg D:92 - Pro D:93	[ RasMol ]
		Glu D:79 - Pro D:80	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
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Access by PDB/NDB ID
	2zho
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	AK_THETH \| P61489
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	2.7.2.4
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UniProtKB/Swiss-Prot
	AK_THETH \| P61489	:	2dt9

2dt9	THE SAME PROTEIN COMPLEXED WITH THREONINE

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, 6)

Exons (0, 0)

Sequences/Alignments

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Pfam Domains (1, 12)

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