1NZY - JenaLib

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Title :   4-CHLOROBENZOYL COENZYME A DEHALOGENASE FROM PSEUDOMONAS SP. STRAIN CBS-3

Authors :   M. M. Benning, H. M. Holden

Date :   02 Apr 96 (Deposition) - 07 Jul 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

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

Reference :   M. M. Benning, K. L. Taylor, R. -. Q. Liu, G. Yang, H. Xiang, G. Wesenberg D. Dunaway-Mariano, H. M. Holden
Structure Of 4-Chlorobenzoyl Coenzyme A Dehalogenase Determined To 1. 8 A Resolution: An Enzyme Catalyst Generate Via Adaptive Mutation.
Biochemistry V. 35 8103 1996
PubMed-ID: 8679561 | Reference-DOI: 10.1021/BI960768P

Molecule 1 - 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
	Chains	:	A, C
	EC Number	:	3.8.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	72586
	Strain	:	CBS-3
	Synonym	:	DEHALOGENASE

Molecule 2 - 4-CHLOROBENZOYL COENZYME A DEHALOGENASE
	Chains	:	B
	EC Number	:	3.8.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PSEUDOMONAS SP. CBS3
	Organism Taxid	:	72586
	Strain	:	CBS-3
	Synonym	:	DEHALOGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	BCA	3	Ligand/Ion	4-HYDROXYBENZOYL COENZYME A
2	CA	3	Ligand/Ion	CALCIUM ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	BCA	6	Ligand/Ion	4-HYDROXYBENZOYL COENZYME A
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	BCA	3	Ligand/Ion	4-HYDROXYBENZOYL COENZYME A
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:49 , LEU A:202 , ALA A:203 , ALA A:205 , THR A:207 , GLN A:210	BINDING SITE FOR RESIDUE CA A 271
2	AC2	SOFTWARE	GLY B:49 , LEU B:202 , ALA B:203 , ALA B:205 , THR B:207 , GLN B:210	BINDING SITE FOR RESIDUE CA B 271
3	AC3	SOFTWARE	GLY C:49 , LEU C:202 , ALA C:203 , ALA C:205 , THR C:207 , GLN C:210	BINDING SITE FOR RESIDUE CA C 271
4	AC4	SOFTWARE	GLU B:57 , ASP B:58 , ASN B:108 , ALA B:128 , LYS B:188 , ARG B:192	BINDING SITE FOR RESIDUE PO4 B 902
5	AC5	SOFTWARE	ARG A:22 , HIS A:23 , ARG A:24 , ALA A:62 , GLY A:63 , PHE A:64 , TYR A:65 , LEU A:66 , ARG A:67 , TRP A:89 , GLY A:113 , GLY A:114 , TRP A:137 , ASP A:145 , THR A:146 , ARG A:251 , ASP A:254 , HIS A:256 , HOH A:313 , HOH A:354 , HOH A:429 , HOH A:432 , HOH A:462 , PHE B:252 , ARG B:257	BINDING SITE FOR RESIDUE BCA A 272
6	AC6	SOFTWARE	ARG B:22 , HIS B:23 , ARG B:24 , ALA B:62 , GLY B:63 , PHE B:64 , TYR B:65 , LEU B:66 , ARG B:67 , TRP B:89 , GLY B:113 , GLY B:114 , TRP B:137 , ASP B:145 , THR B:146 , LYS C:19 , GLU C:57 , PHE C:252 , ALA C:258	BINDING SITE FOR RESIDUE BCA B 272
7	AC7	SOFTWARE	PHE A:252 , ARG A:257 , ALA A:258 , ASP A:259 , ARG C:22 , HIS C:23 , ARG C:24 , ALA C:26 , ALA C:62 , GLY C:63 , PHE C:64 , TYR C:65 , LEU C:66 , ARG C:67 , TRP C:89 , GLY C:113 , GLY C:114 , TRP C:137 , ILE C:140 , ASP C:145 , THR C:146 , HOH C:330 , HOH C:345	BINDING SITE FOR RESIDUE BCA C 272
8	AC8	SOFTWARE	GLU A:201 , PRO A:261 , GLN A:262 , GLU A:264 , HOH A:318 , HOH A:424 , ARG B:251 , HIS B:256	BINDING SITE FOR RESIDUE EDO B 900
9	AC9	SOFTWARE	TYR B:2 , GLU B:3 , ILE B:5	BINDING SITE FOR RESIDUE EDO B 901

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

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	CBADH_PSEUC	104-124	3	A:104-124 B:104-124 C:104-124

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	CBADH_PSEUC	104-124	6	A:104-124 B:104-124 C:104-124

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	CBADH_PSEUC	104-124	3	A:104-124 B:104-124 C:104-124

(no "Exon" information available for 1NZY)

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:269
 aligned with CBADH_PSEUC | A5JTM5 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
          CBADH_PSEUC     1 MYEAIGHRVEDGVAEITIKLPRHRNALSVKAMQEVTDALNRAEEDDSVGAVMITGAEDAFCAGFYLREIPLDKGVAGVRDHFRIGALWWHQMIHKIIRVKRPVLAAINGVAAGGGLGISLASDMAICADSAKFVCAWHTIGIGNDTATSYSLARIVGMRRAMELMLTNRTLYPEEAKDWGLVSRVYPKDDFREVAWKVARELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPCLTEFLDGHRADRPQVELPAGV 269
               SCOP domains d1nzya_ A: 4-Chlorobenzoyl-CoA dehalogenase                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1nzyA01 A:1-204 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                    1nzyA02 A:205-269 Lyase 2-enoyl-coa Hydratase, Chain  A, domain 2 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeee..hhh.....hhhhhhhhhhhhhhhh.....eeeeee..........hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeehhhhhhhhh..eeeee...eee..hhhh.......hhhhhhhhh.hhhhhhhhhh.....hhhhhhh....eee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzy A   1 MYEAIGHRVEDGVAEITIKLPRHRNALSVKAMQEVTDALNRAEEDDSVGAVMITGAEDAFCAGFYLREIPLDKGVAGVRDHFRIAALWWHQMIHKIIRVKRPVLAAINGVAAGGGLGISLASDMAICADSAKFVCAWHTIGIGNDTATSYSLARIVGMRRAMELMLTNRTLYPEEAKDWGLVSRVYPKDEFREVAWKVARELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPCLTRFLDGHRADRPQVELPAGV 269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with CBADH_PSEUC | A5JTM5 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
          CBADH_PSEUC     1 MYEAIGHRVEDGVAEITIKLPRHRNALSVKAMQEVTDALNRAEEDDSVGAVMITGAEDAFCAGFYLREIPLDKGVAGVRDHFRIGALWWHQMIHKIIRVKRPVLAAINGVAAGGGLGISLASDMAICADSAKFVCAWHTIGIGNDTATSYSLARIVGMRRAMELMLTNRTLYPEEAKDWGLVSRVYPKDDFREVAWKVARELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPCLTEFLDGHRADRPQVELPAGV 269
               SCOP domains d1nzyb_ B: 4-Chlorobenzoyl-CoA dehalogenase                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1nzyB01 B:1-204 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                    1nzyB02 B:205-269 Lyase 2-enoyl-coa Hydratase, Chain  A, domain 2 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeee..hhh.....hhhhhhhhhhhhhhhh.....eeeeee..........hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeehhhhhhhhh..eeeee...eee..hhhh.......hhhhhhhhh.hhhhhhhhhh..eeehhhhhhh....eee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzy B   1 MYEAIGHRVEDGVAEITIKLPRHRNALSVKAMQEVTDALNRAEEDDSVGAVMITGAEDAFCAGFYLREIPLDKGVAGVRDHFRIAALWWHQMIHKIIRVKRPVLAAINGVAAGGGLGISLASDMAICADSAKFVCAWHTIGIGNDTATSYSLARIVGMRRAMELMLTDRTLYPEEAKDWGLVSRVYPKDEFREVAWKVARELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPCLTRFLDGHRADRPQVELPAGV 269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain C from PDB  Type:PROTEIN  Length:268
 aligned with CBADH_PSEUC | A5JTM5 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
          CBADH_PSEUC     1 MYEAIGHRVEDGVAEITIKLPRHRNALSVKAMQEVTDALNRAEEDDSVGAVMITGAEDAFCAGFYLREIPLDKGVAGVRDHFRIGALWWHQMIHKIIRVKRPVLAAINGVAAGGGLGISLASDMAICADSAKFVCAWHTIGIGNDTATSYSLARIVGMRRAMELMLTNRTLYPEEAKDWGLVSRVYPKDDFREVAWKVARELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPCLTEFLDGHRADRPQVELPAGV 269
               SCOP domains d1nzyc_ C: 4-Chlorobenzoyl-CoA dehalogenase                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1nzyC01 C:1-204 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                    1nzyC02 C:205-269 Lyase 2-enoyl-coa Hydratase, Chain   A, domain  CATH domains
           Pfam domains (1) -----ECH-1nzyC01 C:6-255                                                                                                                                                                                                                                       -------------- Pfam domains (1)
           Pfam domains (2) -----ECH-1nzyC02 C:6-255                                                                                                                                                                                                                                       -------------- Pfam domains (2)
           Pfam domains (3) -----ECH-1nzyC03 C:6-255                                                                                                                                                                                                                                       -------------- Pfam domains (3)
         Sec.struct. author ....eeeeee..eeeeee..hhh.....hhhhhhhhhhhhhhhh.....eeeeee..........hhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeehhhhhhhhh..eeeee...eee..hhhh.......hhhhhhhhhhhhhhhhhhhh..eeehhhhhhh....eee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhh..-............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzy C   1 MYEAIGHRVEDGVAEITIKLPRHRNALSVKAMQEVTDALNRAEEDDSVGAVMITGAEDAFCAGFYLREIPLDKGVAGVRDHFRIAALWWHQMIHKIIRVKRPVLAAINGVAAGGGLGISLASDMAICADSAKFVCAWHTIGIGNDTATSYSLARIVGMRRAMELMLTNRTLYPEEAKDWGLVSRVYPKDEFREVAWKVARELAAAPTHLQVMAKERFHAGWMQPVEECTEFEIQNVIASVTHPHFMPCLTRFLDGH-ADRPQVELPAGV 269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250     | 260         
                                                                                                                                                                                                                                                                                         256 |           
                                                                                                                                                                                                                                                                                           258

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	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: ClpP/crotonase (207)

Superfamily: ClpP/crotonase (207)

Family: Crotonase-like (39)

Protein domain: 4-Chlorobenzoyl-CoA dehalogenase (2)

Pseudomonas sp., strain CBS-3 [TaxId: 306] (2)

1a	d1nzya_	A:
1b	d1nzyb_	B:
1c	d1nzyc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: 2-enoyl-CoA Hydratase; Chain A, domain 1 (89)

Homologous Superfamily: 2-enoyl-CoA Hydratase; Chain A, domain 1 (89)

Cbs3 (Pseudomonas sp) (2)

1a	1nzyA01	A:1-204
1b	1nzyC01	C:1-204
1c	1nzyB01	B:1-204

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 (25)

Homologous Superfamily: Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 (25)

Cbs3 (Pseudomonas sp) (2)

2a	1nzyC02	C:205-269
2b	1nzyA02	A:205-269
2c	1nzyB02	B:205-269

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ClpP_crotonase (88)

Family: ECH (52)

Pseudomonas sp. (strain CBS-3) (2)

1a	ECH-1nzyC01	C:6-255
1b	ECH-1nzyC02	C:6-255
1c	ECH-1nzyC03	C:6-255

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CBADH_PSEUC | A5JTM5)

molecular function
	GO:0018787	4-chlorobenzoyl-CoA dehalogenase activity	Catalysis of the reaction: 4-chlorobenzoyl-CoA + H2O = 4-hydroxybenzoyl CoA + chloride.
	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: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.
biological process
	GO:0015936	coenzyme A metabolic process	The chemical reactions and pathways involving coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
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(no "Related Entries Specified in the PDB File" available for 1NZY)

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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