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Title :   STRUCTURE OF HALOALCOHOL DEHALOGENASE HHEC OF AGROBACTERIUM RADIOBACTER AD1 IN COMPLEX WITH (R)-PARA-NITRO STYRENE OXIDE, WITH A WATER MOLECULE IN THE HALIDE-BINDING SITE

Authors :   R. M. De Jong, J. J. W. Tiesinga, A. Villa, L. Tang, D. B. Janssen, B. W. Dijkstra

Date :   10 May 05 (Deposition) - 04 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Haloalcohol Dehalogenase, Halohydrin Dehalogenase, Epoxide Catalysis, Enantioselectivity, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. De Jong, J. J. W. Tiesinga, A. Villa, L. Tang, D. B. Janssen, B. W. Dijkstra
Structural Basis For The Enantioselectivity Of An Epoxide Ring Opening Reaction Catalyzed By Halo Alcohol Dehalogenase Hhec.
J. Am. Chem. Soc. V. 127 13338 2005
PubMed-ID: 16173767 | Reference-DOI: 10.1021/JA0531733
(for further references see the PDB file header)

Molecule 1 - HALOALCOHOL DEHALOGENASE HHEC
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PBADHHEC
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358
	Strain	:	AD1

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	RNO	4	Ligand/Ion	(R)-PARA-NITROSTYRENE OXIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE B:12 , PRO B:84 , PHE B:86 , SER B:132 , TRP B:139 , TYR B:145 , PRO B:175 , ASN B:176 , PHE B:186 , TYR B:187 , HOH B:1068 , TRP D:249	BINDING SITE FOR RESIDUE RNO B 1001
2	AC2	SOFTWARE	PRO A:84 , PHE A:86 , SER A:132 , TRP A:139 , TYR A:145 , PRO A:175 , ASN A:176 , PHE A:186 , HOH A:1073 , TRP C:249	BINDING SITE FOR RESIDUE RNO A 1002
3	AC3	SOFTWARE	TRP A:249 , PHE C:12 , PRO C:84 , PHE C:86 , SER C:132 , TRP C:139 , TYR C:145 , PRO C:175 , ASN C:176 , PHE C:186 , TYR C:187 , HOH C:1075	BINDING SITE FOR RESIDUE RNO C 1003
4	AC4	SOFTWARE	TRP B:249 , PHE D:12 , PRO D:84 , PHE D:86 , SER D:132 , TRP D:139 , TYR D:145 , PRO D:175 , ASN D:176 , PHE D:186 , TYR D:187 , HOH D:1072	BINDING SITE FOR RESIDUE RNO D 1004

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

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:185	-	Phe A:186
2	Glu A:190	-	Pro A:191
3	Phe A:243	-	Pro A:244
4	Tyr B:185	-	Phe B:186
5	Glu B:190	-	Pro B:191
6	Phe B:243	-	Pro B:244
7	Tyr C:185	-	Phe C:186
8	Glu C:190	-	Pro C:191
9	Phe C:243	-	Pro C:244
10	Tyr D:185	-	Phe D:186
11	Glu D:190	-	Pro D:191
12	Phe D:243	-	Pro D:244

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

(no "PROSITE Motif" information available for 1ZMT)

(no "Exon" information available for 1ZMT)

Asymmetric/Biological 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:252
 aligned with Q93D82_RHIRD | Q93D82 from UniProtKB/TrEMBL  Length:254

    Alignment length:252
                                    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  
         Q93D82_RHIRD     2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
               SCOP domains d1zmta_ A: Halohydrin dehalogenase HheC                                                                                                                                                                                                                      SCOP domains
               CATH domains 1zmtA00 A:2-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh...ee....hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee............hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhh..eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zmt A   2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
                                    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

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with Q93D82_RHIRD | Q93D82 from UniProtKB/TrEMBL  Length:254

    Alignment length:252
                                    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  
         Q93D82_RHIRD     2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
               SCOP domains d1zmtb_ B: Halohydrin dehalogenase HheC                                                                                                                                                                                                                      SCOP domains
               CATH domains 1zmtB00 B:2-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee............hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhh..eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zmt B   2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
                                    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

Chain C from PDB  Type:PROTEIN  Length:252
 aligned with Q93D82_RHIRD | Q93D82 from UniProtKB/TrEMBL  Length:254

    Alignment length:252
                                    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  
         Q93D82_RHIRD     2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
               SCOP domains d1zmtc_ C: Halohydrin dehalogenase HheC                                                                                                                                                                                                                      SCOP domains
               CATH domains 1zmtC00 C:2-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh...ee....hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee............hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhh..eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zmt C   2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
                                    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

Chain D from PDB  Type:PROTEIN  Length:252
 aligned with Q93D82_RHIRD | Q93D82 from UniProtKB/TrEMBL  Length:254

    Alignment length:252
                                    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  
         Q93D82_RHIRD     2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
               SCOP domains d1zmtd_ D: Halohydrin dehalogenase HheC                                                                                                                                                                                                                      SCOP domains
               CATH domains 1zmtD00 D:2-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee......hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee............hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhh..eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zmt D   2 STAIVTNVKHFGGMGSALRLSEAGHTVACHDESFKQKDELEAFAETYPQLKPMSEQEPAELIEAVTSAYGQVDVLVSNDIFAPEFQPIDKYAVEDYRGAVEALQIRPFALVNAVASQMKKRKSGHIIFITSATPFGPWKELSTYTSARAGACTLANALSKELGEYNIPVFAIGPNYLHSEDSPYFYPTEPWKTNPEHVAHVKKVTALQRLGTQKELGELVAFLASGSCDYLTGQVFWLAGGFPMIERWPGMP 253
                                    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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Halohydrin dehalogenase HheC (5)

Agrobacterium tumefaciens [TaxId: 358] (5)

1a	d1zmta_	A:
1b	d1zmtb_	B:
1c	d1zmtc_	C:
1d	d1zmtd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Agrobacterium tumefaciens. Organism_taxid: 358. Strain: ad1. (2)

1a	1zmtA00	A:2-253
1b	1zmtB00	B:2-253
1c	1zmtC00	C:2-253
1d	1zmtD00	D:2-253

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

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1ZMT)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:190 - Pro A:191	[ RasMol ]
		Glu B:190 - Pro B:191	[ RasMol ]
		Glu C:190 - Pro C:191	[ RasMol ]
		Glu D:190 - Pro D:191	[ RasMol ]
		Phe A:243 - Pro A:244	[ RasMol ]
		Phe B:243 - Pro B:244	[ RasMol ]
		Phe C:243 - Pro C:244	[ RasMol ]
		Phe D:243 - Pro D:244	[ RasMol ]
		Tyr A:185 - Phe A:186	[ RasMol ]
		Tyr B:185 - Phe B:186	[ RasMol ]
		Tyr C:185 - Phe C:186	[ RasMol ]
		Tyr D:185 - Phe D:186	[ RasMol ]

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	1zmt
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	Q93D82_RHIRD \| Q93D82
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	Q93D82_RHIRD \| Q93D82	:	1pwx 1pwz 1px0 1zo8 3zn2 4ixt 4ixw 4iy1 5kvc 5kwe

1zmo	STRUCTURE OF HHEA
1zo8	HHEC IN COMPLEX WITH (S)-PARANITROSTYRENE OXIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

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