1XEY - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF ESCHERICHIA COLI GADA WITH GLUTARATE AT 2.05 A RESOLUTION

Authors :   D. I. Dutyshev, E. L. Darii, N. P. Fomenkova, I. V. Pechik, K. M. Polyakov S. V. Nikonov, N. S. Andreeva, B. S. Sukhareva

Date :   13 Sep 04 (Deposition) - 05 Oct 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Lyase, Glutamate Decarboxylase, Complex With Glutarate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. I. Dutyshev, E. L. Darii, N. P. Fomenkova, I. V. Pechik, K. M. Polyakov, S. V. Nikonov, N. S. Andreeva, B. S. Sukhareva
Structure Of Escherichia Coli Glutamate Decarboxylase (Gadalpha) In Complex With Glutarate At 2. 05 Angstroms Resolution.
Acta Crystallogr. , Sect. D V. 61 230 2005
PubMed-ID: 15735332 | Reference-DOI: 10.1107/S0907444904032147

Molecule 1 - GLUTAMATE DECARBOXYLASE ALPHA
	Chains	:	A, B
	EC Number	:	4.1.1.15
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGAD1
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	GADA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	GAD-ALPHA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GUA	2	Ligand/Ion	GLUTARIC ACID
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	GUA	6	Ligand/Ion	GLUTARIC ACID
3	PLP	6	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:279 , LEU A:334 , VAL A:342 , ARG A:427 , HOH A:859 , SER B:16 , HOH B:858	BINDING SITE FOR RESIDUE ACT A 600
2	AC2	SOFTWARE	SER A:16 , ARG A:17 , PHE A:18 , HOH A:714 , TRP B:67 , VAL B:342 , ARG B:427	BINDING SITE FOR RESIDUE ACT A 700
3	AC3	SOFTWARE	SER A:126 , SER A:127 , GLN A:163 , CYS A:165 , THR A:208 , THR A:212 , ASP A:243 , ALA A:245 , SER A:273 , HIS A:275 , LYS A:276 , HOH A:738 , HOH A:784 , PHE B:317 , SER B:318 , GUA B:505 , HOH B:959	BINDING SITE FOR RESIDUE PLP A 500
4	AC4	SOFTWARE	PHE A:317 , SER A:318 , GUA A:506 , GLY B:125 , SER B:126 , SER B:127 , GLN B:163 , CYS B:165 , THR B:208 , THR B:212 , ASP B:243 , ALA B:245 , SER B:273 , HIS B:275 , LYS B:276 , HOH B:826 , HOH B:879	BINDING SITE FOR RESIDUE PLP B 500
5	AC5	SOFTWARE	THR A:62 , PHE A:63 , GLN A:163 , LYS A:276 , ARG A:422 , PLP A:500 , ASN B:83 , ASP B:86 , GLU B:89 , HOH B:959 , HOH B:1074	BINDING SITE FOR RESIDUE GUA B 505
6	AC6	SOFTWARE	ASN A:83 , ASP A:86 , GLU A:89 , THR B:62 , PHE B:63 , GLN B:163 , LYS B:276 , PLP B:500	BINDING SITE FOR RESIDUE GUA A 506

(no "SS Bond" information available for 1XEY)

(no "Cis Peptide Bond" information available for 1XEY)

(no "SAP(SNP)/Variant" information available for 1XEY)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DDC_GAD_HDC_YDC	PS00392	DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.	DCEA_ECOLI	269-290	2	A:269-290 B:269-290

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DDC_GAD_HDC_YDC	PS00392	DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site.	DCEA_ECOLI	269-290	6	A:269-290 B:269-290

(no "Exon" information available for 1XEY)

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:448
 aligned with DCEA_ECOLI | P69908 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:448
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443        
           DCEA_ECOLI     4 KLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDH 451
               SCOP domains d1xeya_ A: Glutamate decarboxylase alpha, GadA                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....hhhhhh............hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheeeee..eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee........eeeeee........hhhhhhhhhhh......eee.hhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xey A   4 KLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDH 451
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443

Chain B from PDB  Type:PROTEIN  Length:449
 aligned with DCEA_ECOLI | P69908 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:449
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443         
           DCEA_ECOLI     4 KLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHP 452
               SCOP domains d1xeyb_ B: Glutamate decarboxylase alpha, GadA                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------Pyridoxal_deC-1xeyB01 B:33-383                                                                                                                                                                                                                                                                                                                                 --------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------Pyridoxal_deC-1xeyB02 B:33-383                                                                                                                                                                                                                                                                                                                                 --------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh....hhhhhh............hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh..eeee..........hhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh...........eeeeeee...........eeeee.hhhhhhhhhheeeee..eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.........eeeeee........hhhhhhhhhhh......eee........eeeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDC_GAD_HDC_YDC       ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xey B   4 KLLTDFRSELLDSRFGAKAISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHP 452
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: Pyridoxal-dependent decarboxylase (14)

Protein domain: Glutamate decarboxylase alpha, GadA (1)

Escherichia coli [TaxId: 562] (1)

1a	d1xeya_	A:
1b	d1xeyb_	B:

(no "CATH Domain" information available for 1XEY)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Pyridoxal_deC (14)

Escherichia coli (strain K12) (3)

1a	Pyridoxal_deC-1xeyB01	B:33-383
1b	Pyridoxal_deC-1xeyB02	B:33-383

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCEA_ECOLI | P69908)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004351	glutamate decarboxylase activity	Catalysis of the reaction: L-glutamate = 4-aminobutanoate + CO2.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0006536	glutamate metabolic process	The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid.
	GO:0051454	intracellular pH elevation	Any process that increases the internal pH of a cell, measured by the concentration of the hydrogen ion.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Unit
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	1xey
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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