1D7U - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH LCS

Authors :   V. N. Malashkevich, M. D. Toney, P. Strop, J. Keller, J. N. Jansonius

Date :   19 Oct 99 (Deposition) - 19 Nov 99 (Release) - 24 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Enzyme Complexes, Catalytic Mechanism, Decarboxylation Inhibitor, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. N. Malashkevich, P. Strop, J. W. Keller, J. N. Jansonius, M. D. Toney
Crystal Structures Of Dialkylglycine Decarboxylase Inhibito Complexes.
J. Mol. Biol. V. 294 193 1999
PubMed-ID: 10556038 | Reference-DOI: 10.1006/JMBI.1999.3254
(for further references see the PDB file header)

Molecule 1 - PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE))
	Chains	:	A
	EC Number	:	4.1.1.64
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKDHE19
	Expression System Strain	:	TY103
	Expression System Taxid	:	562
	Organism Scientific	:	BURKHOLDERIA CEPACIA
	Organism Taxid	:	292
	Synonym	:	DGD

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	K	1	Ligand/Ion	POTASSIUM ION
2	LCS	1	Ligand/Ion	[5-HYDROXY-6-METHYL-4-({[(4E)-3-OXO-1,2-OXAZOLIDIN-4-YLIDENE]AMINO}METHYL)PYRIDIN-3-YL]METHYL DIHYDROGENPHOSPHATE
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	LCS	4	Ligand/Ion	[5-HYDROXY-6-METHYL-4-({[(4E)-3-OXO-1,2-OXAZOLIDIN-4-YLIDENE]AMINO}METHYL)PYRIDIN-3-YL]METHYL DIHYDROGENPHOSPHATE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:95 , THR A:98 , PRO A:99 , LEU A:102	BINDING SITE FOR RESIDUE NA A 435
2	AC2	SOFTWARE	LEU A:78 , SER A:80 , THR A:303 , VAL A:305 , ASP A:307 , HOH A:529	BINDING SITE FOR RESIDUE K A 436
3	AC3	SOFTWARE	GLN A:52 , THR A:110 , GLY A:111 , ALA A:112 , ASN A:115 , TRP A:138 , HIS A:139 , GLU A:210 , SER A:215 , ASP A:243 , ALA A:245 , GLN A:246 , LYS A:272 , TYR A:301 , THR A:302 , THR A:303 , ARG A:406 , HOH A:504 , HOH A:511 , HOH A:513 , HOH A:602 , HOH A:604 , HOH A:605 , HOH A:674 , HOH A:675	BINDING SITE FOR RESIDUE LCS A 500

(no "SS Bond" information available for 1D7U)

(no "Cis Peptide Bond" information available for 1D7U)

(no "SAP(SNP)/Variant" information available for 1D7U)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_3	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.	DGDA_BURCE	240-277	1	A:240-277

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRANSFER_CLASS_3	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.	DGDA_BURCE	240-277	4	A:240-277

(no "Exon" information available for 1D7U)

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
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Chain A from PDB  Type:PROTEIN  Length:431
 aligned with DGDA_BURCE | P16932 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:431
                                    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       372       382       392       402       412       422       432 
           DGDA_BURCE     3 LNDDATFWRNARQHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSGMLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL 433
               SCOP domains d1d7ua_ A: Dialkylglycine decarboxylase                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------1d7uA01 A:29-60,A:325-433       1d7uA02 A:61-324 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                    1d7uA01 A:29-60,A:325-433 Aspartate Aminotransferase, domain 1                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh...............eeee................hhhhhhhhhhhhhhhhh...eeeeee..ee.....ee...hhhhhhhhhhhhh..eeeee............hhhhhhh....eeee.hhhhh....eeeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhhhhhhhhhh.ee..ee.......eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:240-277   ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d7u A   3 LNDDATFWRNARQHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSGMLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL 433
                                    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       372       382       392       402       412       422       432

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: PLP-dependent transferase-like (627)

Superfamily: PLP-dependent transferases (625)

Family: GABA-aminotransferase-like (167)

Protein domain: Dialkylglycine decarboxylase (13)

Pseudomonas cepacia [TaxId: 292] (13)

d1d7ua_

(no "Pfam Domain" information available for 1D7U)

Asymmetric Unit(hide GO term definitions)

Chain A (DGDA_BURCE | P16932)


GO:0047432	2,2-dialkylglycine decarboxylase (pyruvate) activity	Catalysis of the reaction: 2,2-dialkylglycine + H(+) + pyruvate = L-alanine + CO(2) + dialkyl ketone.
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: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: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.
GO:0008483	transaminase activity	Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.

Asymmetric Unit
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