2J5V - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   GLUTAMATE 5-KINASE FROM ESCHERICHIA COLI COMPLEXED WITH GLUTAMYL-5-PHOSPHATE AND PYROGLUTAMIC ACID

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

Date :   19 Sep 06 (Deposition) - 06 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Proline Biosynthesis, Gamma Glutamyl Kinase, Amino-Acid Biosynthesis, Glutamate Kinase, Kinase, Transferase, Feedback Regulation, Glutamate 5-Kinase, Pua Domain, Amino Acid Kinase, Glutamate, Glutamyl Phosphate, Gamma Glutamyl Phosphate, Proline (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Marco-Marin, F. Gil-Ortiz, I. Perez-Arellano, J. Cervera, I. Fita, V. Rubio
A Novel Two-Domain Architecture Within The Amino Acid Kinase Enzyme Family Revealed By The Crystal Structure Of Escherichia Coli Glutamate 5-Kinase.
J. Mol. Biol. V. 367 1431 2007
PubMed-ID: 17321544 | Reference-DOI: 10.1016/J.JMB.2007.01.073

Molecule 1 - GLUTAMATE 5-KINASE
	Chains	:	A, B
	EC Number	:	2.7.2.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	DH5ALPHA
	Synonym	:	GAMMA-GLUTAMYL KINASE, GK

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	PCA	2	Ligand/Ion	PYROGLUTAMIC ACID
3	RGP	2	Ligand/Ion	GAMMA-GLUTAMYL PHOSPHATE
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:10 , GLY A:12 , LEU A:168 , SO4 A:1371	BINDING SITE FOR RESIDUE MG A1368
2	AC2	SOFTWARE	LYS A:10 , GLY A:12 , THR A:13 , SER A:14 , VAL A:15 , LYS A:217 , MG A:1368 , RGP A:1370 , HOH A:2088 , HOH A:2089	BINDING SITE FOR RESIDUE SO4 A1371
3	AC3	SOFTWARE	LYS B:10 , GLY B:12 , THR B:13 , SER B:14 , VAL B:15 , ASP B:170 , LYS B:217 , RGP B:1369 , HOH B:2075	BINDING SITE FOR RESIDUE SO4 B1370
4	AC4	SOFTWARE	THR A:13 , SER A:50 , GLY A:51 , ALA A:52 , ILE A:53 , ASN A:134 , RGP A:1370	BINDING SITE FOR RESIDUE PCA A1369
5	AC5	SOFTWARE	LYS A:10 , GLY A:12 , THR A:13 , SER A:50 , GLU A:135 , ASP A:137 , LYS A:145 , ASP A:148 , ASN A:149 , PCA A:1369 , SO4 A:1371	BINDING SITE FOR RESIDUE RGP A1370
6	AC6	SOFTWARE	THR B:13 , SER B:50 , GLY B:51 , ALA B:52 , ILE B:53 , ALA B:54 , ASN B:134 , ASP B:137 , RGP B:1369	BINDING SITE FOR RESIDUE PCA B1368
7	AC7	SOFTWARE	LYS B:10 , GLY B:12 , THR B:13 , SER B:50 , GLU B:135 , ASP B:137 , GLY B:147 , ASP B:148 , ASN B:149 , ASP B:150 , PCA B:1368 , SO4 B:1370	BINDING SITE FOR RESIDUE RGP B1369

(no "SS Bond" information available for 2J5V)

(no "Cis Peptide Bond" information available for 2J5V)

(no "SAP(SNP)/Variant" information available for 2J5V)

Asymmetric/Biological Unit (2, 4)

	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:214-224 B:212-224
2	PUA	PS50890	PUA domain profile.	PROB_ECOLI	275-353	2	A:275-353 B:275-353

(no "Exon" information available for 2J5V)

Asymmetric/Biological 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:323
 aligned with PROB_ECOLI | P0A7B5 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:365
                                    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       262       272       282       292       302       312       322       332       342       352       362     
           PROB_ECOLI     3 DSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVMEGISVGTLFHAQATPLENRKRWIFGAPPAGEITVDEGATAAILERGSSLLPKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMITR 367
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhh......hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhh..hhhhhhhhhhhhhh..eeeeee..------------------------------------------hhhhhhhhhhhhhh..eeeeee....hhhhhhhhh....eee.......hhhhhhhhh.....eeeehhhhhhhhhhhh...hhh.eeeee.......eeeeee....eeeeee...hhhhhhhhh..hhhhhhhhhh........hhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAMATE_5_KINASE--------------------------------------------------PUA  PDB: A:275-353 UniProt: 275-353                                           -------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j5v A   3 DSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDNNVVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQ------------------------------------------MSTKLQAADVACRAGIDTIIAAGSKPGVIGDVMEGISVGTLFHAQATPLENRKRWIFGAPPAGEITVDEGATAAILERGSSLLPKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMITR 367
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        |-         -         -         -         - |     222       232       242       252       262       272       282       292       302       312       322       332       342       352       362     
                                                                                                                                                                                                  171                                        214

Chain B from PDB  Type:PROTEIN  Length:325
 aligned with PROB_ECOLI | P0A7B5 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:365
                                    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       262       272       282       292       302       312       322       332       342       352       362     
           PROB_ECOLI     3 DSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDNNIVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQKGLYTADPRSNPQAELIKDVYGIDDALRAIAGDSVSGLGTGGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVMEGISVGTLFHAQATPLENRKRWIFGAPPAGEITVDEGATAAILERGSSLLPKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMITR 367
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeehhhhhhh.....hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhh..hhhhhhhhhhhhh...eeeeee..----------------------------------------hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh....eee.......hhhhhhhhh.....eeeehhhhhhhhhh.....hhh.eeeee.......eeeeee....eeeeeee..hhhhhhhhh..hhhhhhhhhh.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAMATE_5_KINASE--------------------------------------------------PUA  PDB: B:275-353 UniProt: 275-353                                           -------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j5v B   3 DSQTLVVKLGTSVLTGGSRRLNRAHIVELVRQCAQLHAAGHRIVIVTSGAIAAGREHLGYPELPATIASKQLLAAVGQSRLIQLWEQLFSIYGIHVGQMLLTRADMEDRERFLNARDTLRALLDNNVVPVINENDAVATAEIKVGDNDNLSALAAILAGADKLLLLTDQ----------------------------------------GGMSTKLQAADVACRAGIDTIIAAGSKPGVIGDVMEGISVGTLFHAQATPLENRKRWIFGAPPAGEITVDEGATAAILERGSSLLPKGIKSVTGNFSRGEVIRICNLEGRDIAHGVSRYNSDALRRIAGHHSQEIDAILGYEYGPVAVHRDDMITR 367
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        |-         -         -         -       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362     
                                                                                                                                                                                                  171                                      212

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 2J5V)

(no "CATH Domain" information available for 2J5V)

(no "Pfam Domain" information available for 2J5V)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	PROB_ECOLI \| P0A7B5	:	2j5t 2w21

2j5t	GLUTAMATE 5-KINASE FROM ESCHERICHIA COLI COMPLEXED WITH GLUTAMATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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Gene Ontology (13, 13)

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