3C20 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THREONINE-SENSITIVE ASPARTOKINASE FROM METHANOCOCCUS JANNASCHII WITH L-ASPARTATE

Authors :   X. Liu, A. G. Pavlovsky, R. E. Viola

Date :   24 Jan 08 (Deposition) - 29 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Kinase, Allosetric Inhibition, Theronine-Sensitive, Act Domain, Amino-Acid Biosynthesis, Threonine Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Liu, A. G. Pavlovsky, R. E. Viola
The Structural Basis For Allosteric Inhibition Of A Threonine-Sensitive Aspartokinase.
J. Biol. Chem. V. 283 16216 2008
PubMed-ID: 18334478 | Reference-DOI: 10.1074/JBC.M800760200

Molecule 1 - PROBABLE ASPARTOKINASE
	Chains	:	A, B
	EC Number	:	2.7.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET41A
	Expression System Strain	:	ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ0571
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	ASPARTATE KINASE

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	ASP	2	Mod. Amino Acid	ASPARTIC ACID
2	FMT	2	Ligand/Ion	FORMIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID
2	FMT	1	Ligand/Ion	FORMIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID
2	FMT	1	Ligand/Ion	FORMIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:40 , THR B:46 , GLU B:130 , ARG B:207 , GLY B:208 , GLY B:209 , SER B:210	BINDING SITE FOR RESIDUE ASP B 474
2	AC2	SOFTWARE	SER A:40 , THR A:46 , GLU A:130 , PHE A:193 , ARG A:207 , GLY A:208 , GLY A:209 , SER A:210	BINDING SITE FOR RESIDUE ASP A 474
3	AC3	SOFTWARE	ALA A:417 , ILE A:420 , ALA A:421 , GLN A:440	BINDING SITE FOR RESIDUE FMT A 475
4	AC4	SOFTWARE	ALA B:417 , LYS B:418 , GLY B:419 , ILE B:420 , ALA B:421	BINDING SITE FOR RESIDUE FMT B 475

(no "SS Bond" information available for 3C20)

Asymmetric Unit

No.	Residues
1	Phe B:263	-	Gly B:264

(no "SAP(SNP)/Variant" information available for 3C20)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASPARTOKINASE	PS00324	Aspartokinase signature.	AK_METJA	4-12	2	A:4-12 B:4-12
2	ACT	PS51671	ACT domain profile.	AK_METJA	323-392 409-473	4	A:323-392 B:323-392 A:409-470 B:409-470

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASPARTOKINASE	PS00324	Aspartokinase signature.	AK_METJA	4-12	1	A:4-12 -
2	ACT	PS51671	ACT domain profile.	AK_METJA	323-392 409-473	2	A:323-392 - A:409-470 -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASPARTOKINASE	PS00324	Aspartokinase signature.	AK_METJA	4-12	1	- B:4-12
2	ACT	PS51671	ACT domain profile.	AK_METJA	323-392 409-473	2	- B:323-392 - B:409-470

(no "Exon" information available for 3C20)

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:466
 aligned with AK_METJA | Q57991 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:472
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471  
             AK_METJA     2 TTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLEVKERLLPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSETNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEKTNS 473
               SCOP domains d3c20a1 A:2-303 automated matches                                                                                                                                                                                                                                                                             d3c20a2 A:304-403 automated matches                                                                 d3c20a3 A:404-470 automated matches                                  - SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhheee........eeeehhhhhhhhhhhh....eee..eeee....eee...hhhhhhhhhhhhhh...eeeeee....................eehhhhhhhhh.......hhhhhhhhhhhh..eeeee........eee............eeeeeeeeeeeeee.hhhh...hhhhhhhhhhhhh.....eeee.....eeeeeee..hhhhhhhhhhhhh..----.........eeeeeeeeeeeeee.hhhh...hhhhhhhhhhhhh.....eeee.....eeeeeee..hhhhhhhhhhhhhh..--. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ASPARTOKI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: A:323-392 UniProt: 323-392                                  ----------------ACT  PDB: A:409-470 UniProt: 409-473                              PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c20 A   2 TTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLEVKERLLPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSETNISLVVSEEDVDKALKALKREFGD----SFLNNNLIRDVSVDKDVCVISVVGAGMRGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEK--D 474
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381 |    |391       401       411       421       431       441       451       461        |- |
                                                                                                                                                                                                                                                                                                                                                                                                                       383  388                                                                               470  |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 474

Chain B from PDB  Type:PROTEIN  Length:467
 aligned with AK_METJA | Q57991 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:470
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471
             AK_METJA     2 TTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLEVKERLLPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSETNISLVVSEEDVDKALKALKREFGDFGKKSFLNNNLIRDVSVDKDVCVISVVGAGMRGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEKT 471
               SCOP domains d3c20b1 B:2-303 automated matches                                                                                                                                                                                                                                                                             d3c20b2 B:304-403 automated matches                                                                 d3c20b3 B:404-470 automated matches                                - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhheee........eeeehhhhhhhhhhhh....eee..eeee....eee...hhhhhhhhhhhhhh...eeeeee....................eeehhhhhhhh.......hhhhhhhhhhhh..eeeee........eeee...........eeeeeeeeeeeeeehhhhh...hhhhhhhhhhhhh.....eeee......eeeeee..hhhhhhhhhhhhh..---..........eeeeeeeeeeeeee.hhhh...hhhhhhhhhhhhh.....eeee.....eeeeeee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ASPARTOKI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: B:323-392 UniProt: 323-392                                  ----------------ACT  PDB: B:409-470 UniProt: 409-473                            PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c20 B   2 TTVMKFGGTSVGSGERIRHVAKIVTKRKKEDDDVVVVVSAMSEVTNALVEISQQALDVRDIAKVGDFIKFIREKHYKAIEEAIKSEEIKEEVKKIIDSRIEELEKVLIGVAYLGELTPKSRDYILSFGERLSSPILSGAIRDLGEKSIALEGGEAGIITDNNFGSARVKRLEVKERLLPLLKEGIIPVVTGFIGTTEEGYITTLGRGGSDYSAALIGYGLDADIIEIWTDVSGVYTTDPRLVPTARRIPKLSYIEAMELAYFGAKVLHPRTIEPAMEKGIPILVKNTFEPESEGTLITNDMEMSDSIVKAISTIKNVALINIFGAGMVGVSGTAARIFKALGEEEVNVILISQGSSETNISLVVSEEDVDKALKALKREFGD---KSFLNNNLIRDVSVDKDVCVISVVGAGMRGAKGIAGKIFTAVSESGANIKMIAQGSSEVNISFVIDEKDLLNCVRKLHEKFIEKD 474
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381 |   | 391       401       411       421       431       441       451       461       474
                                                                                                                                                                                                                                                                                                                                                                                                                       383 387                                                                                470|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               474

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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: ACT-like (63)

Family: automated matches (16)

Protein domain: automated matches (16)

Methanocaldococcus jannaschii [TaxId: 2190] (3)

1a	d3c20a2	A:304-403
1b	d3c20b2	B:304-403
1c	d3c20b3	B:404-470
1d	d3c20a3	A:404-470

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

Fold: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

Family: PyrH-like (22)

Protein domain: automated matches (11)

Methanocaldococcus jannaschii [TaxId: 2190] (3)

2a	d3c20a1	A:2-303
2b	d3c20b1	B:2-303

(no "CATH Domain" information available for 3C20)

(no "Pfam Domain" information available for 3C20)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AK_METJA | Q57991)

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: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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	Cis Peptide Bonds
		Phe B:263 - Gly B:264	[ RasMol ]

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	3c20
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	2.7.2.4
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	AK_METJA \| Q57991	:	2hmf 3c1m 3c1n

Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (0, 0)

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