2W21 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE AMINOACID KINASE DOMAIN OF THE GLUTAMATE 5 KINASE OF ESCHERICHIA COLI.

Authors :   I. Perez-Arellano, F. Gil-Ortiz, C. Marco-Marin, J. Cervera, V. Rubio

Date :   21 Oct 08 (Deposition) - 17 Nov 09 (Release) - 17 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

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

Keywords :   Amino Acid Kinase Family, Proline Biosynthesis, Amino-Acid Biosynthesis, Kinase, Cytoplasm, Transferase, Glutamate Kinaseamino Acid Kinase Family, Glutamate Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Perez-Arellano, F. Gil-Ortiz, C. Marco-Marin, J. Cervera, V. Rubio
The Structure Of Glutamate 5 Kinase Of Escherichia Coli Without Substrates
To Be Published
PubMed: search

Molecule 1 - GLUTAMATE 5-KINASE
	Chains	:	A
	EC Number	:	2.7.2.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	AMINO ACID KINASE DOMAIN, RESIDUES 1-259
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	511693
	Synonym	:	GAMMA-GLUTAMYL KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , THR A:13 , SER A:14 , VAL A:15 , THR A:169 , ASP A:170 , LYS A:217 , HOH A:2002	BINDING SITE FOR RESIDUE SO4 A1259
2	AC2	SOFTWARE	LYS A:10 , SER A:50 , VAL A:146 , GLY A:147 , ASP A:148 , ASN A:149 , ASP A:150	BINDING SITE FOR RESIDUE SO4 A1260
3	AC3	SOFTWARE	THR A:104 , ARG A:105 , ALA A:106 , ARG A:113 , THR A:141 , ALA A:142	BINDING SITE FOR RESIDUE SO4 A1261
4	AC4	SOFTWARE	THR A:13 , SER A:50 , GLY A:51 , ALA A:52 , ILE A:53 , ALA A:54	BINDING SITE FOR RESIDUE SO4 A1262

(no "SS Bond" information available for 2W21)

(no "Cis Peptide Bond" information available for 2W21)

(no "SAP(SNP)/Variant" information available for 2W21)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAMATE_5_KINASE	PS00902	Glutamate 5-kinase signature.	PROB_ECOLI	207-224	1	A:212-224

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLUTAMATE_5_KINASE	PS00902	Glutamate 5-kinase signature.	PROB_ECOLI	207-224	2	A:212-224

(no "Exon" information available for 2W21)

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:246
 aligned with PROB_ECOLI | P0A7B5 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:256
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      
           PROB_ECOLI     3 DSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVMEGISVGTLFHAQ 258
               SCOP domains d2w21a_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --AA_kinase-2w21A01 A:5-235                                                                                                                                                                                                              ----------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhh......hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......-...hhhhhhhhhhhhhh...eeeeee....................eeehhhhhhhhh.---------.hhhhhhhhhhhhhh...eeeeee....hhhhhhhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAMATE_5_KINASE---------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w21 A   3 DSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDNNVVPVINENDAVATA-IKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAELIKDVYGIDDALRAIA---------GGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVMEGISVGTLFHAQ 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142 |     152       162       172       182       192       202       212       222       232       242       252      
                                                                                                                                                                     142 |                                                       202       212                                              
                                                                                                                                                                       144

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: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

Family: automated matches (24)

Protein domain: automated matches (24)

Escherichia coli [TaxId: 511693] (1)

d2w21a_

(no "CATH Domain" information available for 2W21)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: AA_kinase] (20)

Family: AA_kinase (20)

Escherichia coli (strain K12) (5)

AA_kinase-2w21A01

A:5-235

Asymmetric Unit(hide GO term definitions)

Chain A (PROB_ECOLI | P0A7B5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004349	glutamate 5-kinase activity	Catalysis of the reaction: L-glutamate + ATP = L-glutamyl 5-phosphate + ADP + H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) 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: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:0055129	L-proline biosynthetic process	The chemical reactions and pathways resulting in the formation of L-proline, an L-enantiomer of a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
	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: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:0006561	proline biosynthetic process	The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Biological Unit
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	2w21
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	2.7.2.11
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UniProtKB/Swiss-Prot
	PROB_ECOLI \| P0A7B5	:	2j5t 2j5v

2j5t	GLUTAMATE 5-KINASE FROM ESCHERICHIA COLI COMPLEXED WITH GLUTAMATE
2j5v	GLUTAMATE 5-KINASE FROM ESCHERICHIA COLI COMPLEXED WITH GLUTAMYL-5-PHOSPHATE AND PYROGLUTAMIC ACID

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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