3DQZ - JenaLib

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Title :   STRUCTURE OF THE HYDROXYNITRILE LYASE FROM ARABIDOPSIS THALIANA

Authors :   J. Andexer, N. Staunig, K. Gruber

Date :   10 Jul 08 (Deposition) - 14 Jul 09 (Release) - 23 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   A/B-Hydrloase Fold, Cyanogenesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. N. Andexer, N. Staunig, T. Eggert, C. Kratky, M. Pohl, K. Gruber
Hydroxynitrile Lyases With Alpha / Beta-Hydrolase Fold: Two Enzymes With Almost Identical 3D Structures But Opposite Enantioselectivities And Different Reaction Mechanisms
Chembiochem V. 13 1932 2012
PubMed-ID: 22851196 | Reference-DOI: 10.1002/CBIC.201200239

Molecule 1 - ALPHA-HYDROXYNITRILE LYASE-LIKE PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	F18D22_70, AT5G10300
	Organism Common	:	MOUSE-EAR CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	ATHNL, AT5G10300/F18D22_70

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG D:175 , GLN D:176	BINDING SITE FOR RESIDUE CL D 259

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

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

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

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

(no "Exon" information available for 3DQZ)

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:256
 aligned with HNL_ARATH | Q9LFT6 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    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      
            HNL_ARATH     3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDYM 258
               SCOP domains d3dqza_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3dqzA00 A:3-258  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhh.hhh.eeeeeee...........hhhhhhhhh........eeeeeee..eeeeeee.hhhhhhhhh....hhhhhhhhhhhh..ee.hhhhhhh.......hhhhh.eeeeee......hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dqz A   3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDYM 258
                                    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

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with HNL_ARATH | Q9LFT6 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:255
                                    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     
            HNL_ARATH     3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDY 257
               SCOP domains d3dqzb_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3dqzB00 B:3-257  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhh.eeeeeee...........hhhhhhhhh........eeeeeee..eeeeeee.hhhhhhhhh....hhhhhhhhhh....ee.hhhhhhh.......hhhhheeeeeee......hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dqz B   3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDY 257
                                    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

Chain C from PDB  Type:PROTEIN  Length:256
 aligned with HNL_ARATH | Q9LFT6 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:256
                                    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      
            HNL_ARATH     3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDYM 258
               SCOP domains d3dqzc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3dqzC00 C:3-258  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhh.hhh.eeeeeee...........hhhhhhhhh........eeeeeee..eeeeeee.hhhhhhhhh....hhhhhhhhhhhh..ee.hhhhhhh.......hhhhh.eeeeee......hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dqz C   3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDYM 258
                                    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

Chain D from PDB  Type:PROTEIN  Length:255
 aligned with HNL_ARATH | Q9LFT6 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:255
                                    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     
            HNL_ARATH     3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDY 257
               SCOP domains d3dqzd_ D: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3dqzD00 D:3-257  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeee.hhhhhhhhhhh.hhh.eeeeeee...........hhhhhhhhh........eeeeeee..eeeeeee.hhhhhhhhh....hhhhhhhhhh....ee.hhhhhhh.......hhhhh.eeeeee......hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dqz D   3 RKHHFVLVHNAYHGAWIWYKLKPLLESAGHRVTAVELAASGIDPRPIQAVETVDEYSKPLIETLKSLPENEEVILVGFSFGGINIALAADIFPAKIKVLVFLNAFLPDTTHVPSHVLDKYMEMPGGLGDCEFSSHETRNGTMSLLKMGPKFMKARLYQNCPIEDYELAKMLHRQGSFFTEDLSKKEKFSEEGYGSVQRVYVMSSEDKAIPCDFIRWMIDNFNVSKVYEIDGGDHMVMLSKPQKLFDSLSAIATDY 257
                                    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

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: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: automated matches (184)

Protein domain: automated matches (184)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (8)

1a	d3dqza_	A:
1b	d3dqzb_	B:
1c	d3dqzc_	C:
1d	d3dqzd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Mouse-ear cress (Arabidopsis thaliana) (1)

1a	3dqzA00	A:3-258
1b	3dqzC00	C:3-258
1c	3dqzB00	B:3-257
1d	3dqzD00	D:3-257

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HNL_ARATH | Q9LFT6)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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:0046593	mandelonitrile lyase activity	Catalysis of the reaction: mandelonitrile = cyanide + benzaldehyde.
	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).
biological process
	GO:0016139	glycoside catabolic process	The chemical reactions and pathways resulting in the breakdown of glycosides, compounds in which a glycosyl group is substituted into a hydroxyl, thiol or selenol group in another compound.
	GO:0009611	response to wounding	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.

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Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

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