1ZOB - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASES BOUND WITH CALCIUM ION

Authors :   W. Liu, M. D. Toney

Date :   12 May 05 (Deposition) - 08 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (4x)

Keywords :   Decarboxylase, Pyridoxal Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Liu, M. D. Toney
Crystal Structures Of Dialkylglycine Decarboxylase Bound With Cesium Ion And Calcium Ion
To Be Published
PubMed: search

Molecule 1 - 2,2-DIALKYLGLYCINE DECARBOXYLASE
	Chains	:	A
	EC Number	:	4.1.1.64
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBTAC
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BURKHOLDERIA CEPACIA
	Organism Taxid	:	292
	Synonym	:	DGD

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	NA	1	Ligand/Ion	SODIUM ION
4	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	NA	-1	Ligand/Ion	SODIUM ION
4	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MES	4	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	NA	-1	Ligand/Ion	SODIUM ION
4	PLP	4	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:95 , THR A:98 , PRO A:99 , LEU A:102 , HOH A:500	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:481 , HOH A:482	BINDING SITE FOR RESIDUE CA A 436
3	AC3	SOFTWARE	THR A:110 , ALA A:112 , ASN A:115 , TRP A:138 , HIS A:139 , GLU A:210 , ASP A:243 , ALA A:245 , GLN A:246 , LYS A:272 , THR A:302 , THR A:303 , HOH A:478 , HOH A:489 , HOH A:490	BINDING SITE FOR RESIDUE PLP A 434
4	AC4	SOFTWARE	TRP A:138 , SER A:215 , GLN A:246 , LYS A:272 , TYR A:301 , ARG A:406 , HOH A:442 , HOH A:479	BINDING SITE FOR RESIDUE MES A 437

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

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

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

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, 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 2 (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 1ZOB)

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: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 d1zoba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------1zobA01 A:29-60,A:325-433       1zobA02 A:61-324 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                    1zobA01 A:29-60,A:325-433 Aspartate Aminotransferase, domain 1                                                CATH domains
               Pfam domains -------------------------Aminotran_3-1zobA01 A:28-367                                                                                                                                                                                                                                                                                                                        ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.............eee..eee.....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh................eeee..................hhhhhhhhhhhhhhh...eeeeee..ee.....ee...hhhhhhhhhhhhh..eeeee.............hhhhhh....eeeehhhhhh....eeeeeehhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeeee....ee..hhhhhhhhhhhhh.ee..eee.....eeeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:240-277   ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zob A   3 LNDDATFWRNARHHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSEMLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL 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(

)

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: GABA-aminotransferase-like (167)

Protein domain: automated matches (28)

Burkholderia cepacia [TaxId: 292] (3)

d1zoba_

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PLP_aminotran (240)

Family: Aminotran_3 (44)

Burkholderia cepacia (Pseudomonas cepacia) (7)

Aminotran_3-1zobA01

A:28-367

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zob)

Biological Units
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1dka	DIALKYLGLYCINE DECARBOXYLASE COMPLEX WITH POTASSIUM ION
1zod
2dkb	DIALKYLGLYCINE DECARBOXYLASE COMPLEX WITH SODIUM ION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

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