3C6Y - JenaLib

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Title :   HNL FROM HEVEA BRASILIENSIS TO ATOMIC RESOLUTION

Authors :   A. Schmidt

Date :   06 Feb 08 (Deposition) - 03 Jun 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

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

Keywords :   Atomic Resolution, Hydroxynitril Lyase, Catalysis, Protonation State, Ab Initio Calculations, Substrate Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Schmidt, K. Gruber, C. Kratky, V. S. Lamzin
Atomic Resolution Crystal Structures And Quantum Chemistry Meet To Reveal Subtleties Of Hydroxynitrile Lyase Catalysis
J. Biol. Chem. V. 283 21827 2008
PubMed-ID: 18524775 | Reference-DOI: 10.1074/JBC.M801056200
(for further references see the PDB file header)

Molecule 1 - HYDROXYNITRILASE
	Chains	:	A
	EC Number	:	4.1.2.37
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	BHIL-D2
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PLASMID
	Gene	:	HNL
	Organism Common	:	PARA RUBBER TREE
	Organism Scientific	:	HEVEA BRASILIENSIS
	Organism Taxid	:	3981
	Synonym	:	(S)-ACETONE-CYANOHYDRIN LYASE, (S)-HYDROXYNITRILE LYASE, OXYNITRILASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ACN	1	Ligand/Ion	ACETONE
2	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 14)

No.	Name	Count	Type	Full Name
1	ACN	2	Ligand/Ion	ACETONE
2	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
3	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:23 , LYS A:170 , HOH A:3019 , HOH A:3134 , HOH A:3172 , HOH A:3249 , HOH A:3444 , HOH A:3495 , HOH A:3530	BINDING SITE FOR RESIDUE SO4 A 2001
2	AC2	SOFTWARE	THR A:137 , LYS A:138 , ASP A:139 , GLY A:140 , GLY A:232 , GLY A:233 , LYS A:241 , HOH A:3224 , HOH A:3236 , HOH A:3340 , HOH A:3380	BINDING SITE FOR RESIDUE SO4 A 2002
3	AC3	SOFTWARE	LYS A:141 , ASN A:181 , LYS A:185 , HOH A:3115 , HOH A:3128 , HOH A:3142 , HOH A:3421 , HOH A:3488	BINDING SITE FOR RESIDUE SO4 A 2003
4	AC4	SOFTWARE	THR A:110 , GLY A:195 , TYR A:222 , HOH A:3257 , HOH A:3471	BINDING SITE FOR RESIDUE SO4 A 2004
5	AC5	SOFTWARE	CYS A:94 , GLU A:95 , GLU A:192 , HOH A:3356	BINDING SITE FOR RESIDUE BME A 2005
6	AC6	SOFTWARE	THR A:11 , ILE A:12 , SER A:80 , TRP A:128 , LEU A:148 , LEU A:157 , HIS A:235 , HOH A:3050	BINDING SITE FOR RESIDUE ACN A 1001
7	AC7	SOFTWARE	GLN A:47 , LYS A:147 , ARG A:174 , LYS A:175 , HOH A:3149 , HOH A:3324 , HOH A:3455	BINDING SITE FOR RESIDUE PEG A 1501

(no "SS Bond" information available for 3C6Y)

(no "Cis Peptide Bond" information available for 3C6Y)

(no "SAP(SNP)/Variant" information available for 3C6Y)

(no "PROSITE Motif" information available for 3C6Y)

(no "Exon" information available for 3C6Y)

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)
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Chain A from PDB  Type:PROTEIN  Length:256
 aligned with HNL_HEVBR | P52704 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      
            HNL_HEVBR     2 AFAHFVLIHTICHGAWIWHKLKPLLEALGHKVTALDLAASGVDPRQIEEIGSFDEYSEPLLTFLEALPPGEKVILVGESCGGLNIAIAADKYCEKIAAAVFHNSVLPDTEHCPSYVVDKLMEVFPDWKDTTYFTYTKDGKEITGLKLGFTLLRENLYTLCGPEEYELAKMLTRKGSLFQNILAKRPFFTKEGYGSIKKIYVWTDQDEIFLPEFQLWQIENYKPDKVYKVEGGDHKLQLTKTKEIAEILQEVADTYN 257
               SCOP domains d3c6ya_ A: Hydroxynitrile lyase                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3c6yA00 A:2-257  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh..eeeee..........hhhhh.hhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhh..eeeeeeeee.........hhhhhhhhhhh......eeeeeee..eeeeeee.hhhhhhhhh....hhhhhhhhhhhh..ee.hhhhhhhh......hhhhh.eeeee.......hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c6y A   2 AFAHFVLIHTICHGAWIWHKLKPLLEALGHKVTALDLAASGVDPRQIEEIGSFDEYSEPLLTFLEALPPGEKVILVGESCGGLNIAIAADKYCEKIAAAVFHNSVLPDTEHCPSYVVDKLMEVFPDWKDTTYFTYTKDGKEITGLKLGFTLLRENLYTLCGPEEYELAKMLTRKGSLFQNILAKRPFFTKEGYGSIKKIYVWTDQDEIFLPEFQLWQIENYKPDKVYKVEGGDHKLQLTKTKEIAEILQEVADTYN 257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

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( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Hydroxynitrile lyase-like (34)

Protein domain: Hydroxynitrile lyase (28)

Rubber tree (Hevea brasiliensis) [TaxId: 3981] (19)

d3c6ya_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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)

Para rubber tree (Hevea brasiliensis) (5)

3c6yA00

A:2-257

(no "Pfam Domain" information available for 3C6Y)

Asymmetric Unit(hide GO term definitions)

Chain A (HNL_HEVBR | P52704)


GO:0052891	aliphatic (S)-hydroxynitrile lyase activity	Catalysis of the reaction: an aliphatic (S)-hydroxynitrile = an aliphatic aldehyde or ketone + cyanide.
GO:0052892	aromatic (S)-hydroxynitrile lyase activity	Catalysis of the reaction: an aromatic (S)-hydroxynitrile = an aromatic aldehyde + cyanide.
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.

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	Cis Peptide Bonds
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	3c6y
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	4.1.2.37
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1qj4	HNL AT ATOMIC RESOLUTION
3c6x	HNL FROM HEVEA BRASILIENSIS TO ATOMIC RESOLUTION, NATIVE WITH PEG200
3c6z	HNL FROM HEVEA BRASILIENSIS TO ATOMIC RESOLUTION, COMPLEX WITH ISOPROPANOL
3c70	HNL FROM HEVEA BRASILIENSIS TO ATOMIC RESOLUTION, COMPLEX WITH RHODANIDE (SCN)
7yas	HNL LOW TEMPERATURE NATIVE STRUCTURE

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Ligands, Modified Residues, Ions (4, 7)

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