3DTV - JenaLib

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Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ARYLMALONATE DECARBOXYLASE

Authors :   M. Nakasako, R. Obata, K. Miyamaoto, H. Ohta

Date :   16 Jul 08 (Deposition) - 21 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A (1x),B (1x),C (1x),D (1x)

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

Reference :   R. Obata, M. Nakasako
Structural Basis For Inverting The Enantioselectivity Of Arylmalonate Decarboxylase Revealed By The Structural Analysis Of The Gly74Cys/Cys188Ser Mutant In The Liganded Form
Biochemistry V. 49 1963 2010
PubMed-ID: 20136121 | Reference-DOI: 10.1021/BI9015605
(for further references see the PDB file header)

Molecule 1 - ARYLMALONATE DECARBOXYLASE
	Chains	:	A
	EC Number	:	4.1.1.76
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAMD 101
	Expression System Strain	:	DH5ALPHA-MCR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	ALCALIGENES BRONCHISEPTICUS
	Organism Scientific	:	BORDETELLA BRONCHISEPTICA
	Organism Taxid	:	518
	Strain	:	KU1201
	Synonym	:	AMDASE

Molecule 2 - ARYLMALONATE DECARBOXYLASE
	Chains	:	B, C
	EC Number	:	4.1.1.76
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAMD 101
	Expression System Strain	:	DH5ALPHA-MCR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	ALCALIGENES BRONCHISEPTICUS
	Organism Scientific	:	BORDETELLA BRONCHISEPTICA
	Organism Taxid	:	518
	Synonym	:	AMDASE

Molecule 3 - ARYLMALONATE DECARBOXYLASE
	Chains	:	D
	EC Number	:	4.1.1.76
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAMD 101
	Expression System Strain	:	DH5ALPHA-MCR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	ALCALIGENES BRONCHISEPTICUS
	Organism Scientific	:	BORDETELLA BRONCHISEPTICA
	Organism Taxid	:	518
	Synonym	:	AMDASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CME	3	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	GOL	4	Ligand/Ion	GLYCEROL
4	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	BME	-1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CME	-1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	BME	-1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	BME	-1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 5 (2, 5)

No.	Name	Count	Type	Full Name
1	BME	-1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CME	-1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:61 , PRO B:100 , LEU B:222 , SO4 B:1005	BINDING SITE FOR RESIDUE SO4 A 1000
02	AC2	SOFTWARE	GLY A:74 , THR A:75 , SER A:76 , TYR A:126 , CYS A:188 , GLY A:189 , HOH A:1155	BINDING SITE FOR RESIDUE SO4 A 1001
03	AC3	SOFTWARE	ARG A:94 , PRO A:100 , CYS A:101 , GOL A:1100 , HOH A:1173	BINDING SITE FOR RESIDUE SO4 A 1002
04	AC4	SOFTWARE	ARG A:149 , ARG A:173	BINDING SITE FOR RESIDUE SO4 A 1003
05	AC5	SOFTWARE	SO4 A:1002 , THR C:154 , ASP D:49	BINDING SITE FOR RESIDUE GOL A 1100
06	AC6	SOFTWARE	VAL B:43 , THR B:44 , ARG B:81 , BME B:1101	BINDING SITE FOR RESIDUE SO4 B 1004
07	AC7	SOFTWARE	SO4 A:1000 , ARG B:94 , PRO B:100 , CYS B:101 , HOH B:1178	BINDING SITE FOR RESIDUE SO4 B 1005
08	AC8	SOFTWARE	ILE B:127 , ASP B:128 , GLY B:152	BINDING SITE FOR RESIDUE SO4 B 1006
09	AC9	SOFTWARE	THR B:44 , GLY B:47 , TYR B:48 , SO4 B:1004 , GLU C:140	BINDING SITE FOR RESIDUE BME B 1101
10	BC1	SOFTWARE	PRO B:14 , THR B:75 , SER B:76	BINDING SITE FOR RESIDUE GOL B 1102
11	BC2	SOFTWARE	PRO C:14 , GLY C:74 , THR C:75 , SER C:76 , GLY C:189 , HOH C:1160 , HOH C:1174 , HOH C:1190 , VAL D:43 , THR D:44 , GOL D:1104	BINDING SITE FOR RESIDUE SO4 C 1007
12	BC3	SOFTWARE	ASP C:163 , THR C:164 , HOH C:1172	BINDING SITE FOR RESIDUE SO4 C 1008
13	BC4	SOFTWARE	ALA C:50 , GLU C:53 , SER C:54 , ASP C:57	BINDING SITE FOR RESIDUE GOL C 1103
14	BC5	SOFTWARE	ARG D:149 , ARG D:173	BINDING SITE FOR RESIDUE SO4 D 1009
15	BC6	SOFTWARE	ALA C:125 , GLY C:189 , GLY C:190 , SO4 C:1007 , THR D:44 , PRO D:45 , GLU D:46	BINDING SITE FOR RESIDUE GOL D 1104

(no "SS Bond" information available for 3DTV)

(no "Cis Peptide Bond" information available for 3DTV)

(no "SAP(SNP)/Variant" information available for 3DTV)

(no "PROSITE Motif" information available for 3DTV)

(no "Exon" information available for 3DTV)

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:217
 aligned with AMDA_BORBO | Q05115 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:234
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    
           AMDA_BORBO     7 PTIGMIVPPAAGLVPADGARLYPDLPFIASGLGLGSVTPEGYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGCRSLGITGVEAMARVDTATLVDLCVRAFEAAPDSDGILLSCGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFDES 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee........hhhhhhh....eeeee..------.hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..eeeeeee.-----------hhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhh..eeehhhhhhhhhhhhhh.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dtv A   7 PTIGMIVPPAAGLVPADGARLYPDLPFIASGLG------EGYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGCRSL-----------DTATLVDLCVRAFEAAPDSDGILLSCGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFDES 240
                                    16        26        36  |     46        56        66        76        86        96       106       116       126       136       146    |    -      |166       176       186       196       206       216       226       236    
                                                           39     46                                                                                                      151         163

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with AMDA_BORBO | Q05115 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:234
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234    
           AMDA_BORBO     5 STPTIGMIVPPAAGLVPADGARLYPDLPFIASGLGLGSVTPEGYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGCRSLGITGVEAMARVDTATLVDLCVRAFEAAPDSDGILLSCGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFD 238
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.........hhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh..eeeeeee..hhhhhh....hhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhh..eeehhhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dtv B   5 STPTIGMIVPPAAGLVPADGARLYPDLPFIASGLGLGSVTPEGYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGcRSLGITGVEAMARVDTATLVDLCVRAFEAAPDSDGILLSCGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFD 238
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144   |   154       164       174       184       194       204       214       224       234    
                                                                                                                                                                         148-CME

Chain C from PDB  Type:PROTEIN  Length:228
 aligned with AMDA_BORBO | Q05115 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:234
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236    
           AMDA_BORBO     7 PTIGMIVPPAAGLVPADGARLYPDLPFIASGLGLGSVTPEGYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGCRSLGITGVEAMARVDTATLVDLCVRAFEAAPDSDGILLSCGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFDES 240
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee........hhhhhhh....eeeee...------hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhh.hhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..eeeeeee....hhhhhhh.hhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhh..eeehhhhhhhhhhhhhh.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dtv C   7 PTIGMIVPPAAGLVPADGARLYPDLPFIASGLGL------GYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGcRSLGITGVEAMARVDTATLVDLCVRAFEAAPDSDGILLSCGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFDES 240
                                    16        26        36   |     -|       56        66        76        86        96       106       116       126       136       146 |     156       166       176       186       196       206       216       226       236    
                                                            40     47                                                                                                  148-CME

Chain D from PDB  Type:PROTEIN  Length:236
 aligned with AMDA_BORBO | Q05115 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:236
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
           AMDA_BORBO     5 STPTIGMIVPPAAGLVPADGARLYPDLPFIASGLGLGSVTPEGYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGCRSLGITGVEAMARVDTATLVDLCVRAFEAAPDSDGILLSCGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFDES 240
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhh......eeeee.hhhh....hhhhhhhhhhhhhhhhhhh...eeee..hhhhh..hhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhh..eeeeeee....hhhhhh..hhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhh..eeehhhhhhhhhhhhhh.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dtv D   5 STPTIGMIVPPAAGLVPADGARLYPDLPFIASGLGLGSVTPEGYDAVIESVVDHARRLQKQGAAVVSLMGTSLSFYRGAAFNAALTVAMREATGLPCTTMSTAVLNGLRALGVRRVALATAYIDDVNERLAAFLAEESLVPTGCRSLGITGVEAMARVDTATLVDLCVRAFEAAPDSDGILLScGGLLTLDAIPEVERRLGVPVVSSSPAGFWDAVRLAGGGAKARPGYGRLFDES 240
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184   |   194       204       214       224       234      
                                                                                                                                                                                                                 188-CME

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3DTV)

(no "CATH Domain" information available for 3DTV)

(no "Pfam Domain" information available for 3DTV)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (AMDA_BORBO | Q05115)

molecular function
	GO:0047436	arylmalonate decarboxylase activity	Catalysis of the reaction: 2-aryl-2-methylmalonate + H(+) = 2-arylpropionate + CO(2).
	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.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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	3dtv
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	AMDA_BORBO \| Q05115	:	2vlb 3dg9 3eis 3ip8 3ixl 3ixm

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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