3EJ3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURAL AND MECHANISTIC ANALYSIS OF TRANS-3-CHLOROACRYLIC ACID DEHALOGENASE ACTIVITY

Authors :   S. Pegan, H. Serrano, C. P. Whitman, A. D. Mesecar

Date :   17 Sep 08 (Deposition) - 02 Dec 08 (Release) - 02 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F  (1x)
Biol. Unit 2: G,H,I,J,K,L  (1x)

Keywords :   Trans-3-Chloroacrylic Acid Dehalogenase, Caad, Dehalogenase, Isomerase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Pegan, H. Serrano, C. P. Whitman, A. D. Mesecar
Structural And Mechanistic Analysis Of Trans-3-Chloroacrylic Acid Dehalogenase Activity.
Acta Crystallogr. , Sect. D V. 64 1277 2008
PubMed-ID: 19018104 | Reference-DOI: 10.1107/S0907444908034707
(for further references see the PDB file header)

Molecule 1 - ALPHA-SUBUNIT OF TRANS-3-CHLOROACRYLIC ACID DEHALOGENASE
	Chains	:	A, C, E, G, I, K
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CAAD1
	Organism Scientific	:	PSEUDOMONAS PAVONACEAE
	Organism Taxid	:	47881

Molecule 2 - BETA-SUBUNIT OF TRANS-3-CHLOROACRYLIC ACID DEHALOGENASE
	Chains	:	B, D, F, H, J, L
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CAAD2
	Organism Scientific	:	PSEUDOMONAS PAVONACEAE
	Organism Taxid	:	47881

		1	2	3	4	5	6	7	8	9	10	11	12
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J	K	L
Biological Unit 1 (1x)	:	A	B	C	D	E	F
Biological Unit 2 (1x)	:							G	H	I	J	K	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:8 , ARG A:11 , PHE A:50 , PRO D:1	BINDING SITE FOR RESIDUE ACT A 76
2	AC2	SOFTWARE	ARG A:43 , GLU B:4 , HOH B:89 , HOH B:92 , HOH B:95 , ARG C:43 , GLU D:4 , ARG E:43 , GLU F:4 , HOH F:101	BINDING SITE FOR RESIDUE PO4 B 71
3	AC3	SOFTWARE	ARG C:8 , ARG C:11 , PHE C:50 , GLU C:52 , PRO F:1	BINDING SITE FOR RESIDUE ACT C 76
4	AC4	SOFTWARE	PRO B:1 , ILE B:37 , ARG E:8 , ARG E:11 , PHE E:50	BINDING SITE FOR RESIDUE ACT E 76
5	AC5	SOFTWARE	ARG G:8 , ARG G:11 , PRO J:1	BINDING SITE FOR RESIDUE ACT G 76
6	AC6	SOFTWARE	ARG I:8 , ARG I:11 , PRO L:1	BINDING SITE FOR RESIDUE ACT I 76
7	AC7	SOFTWARE	ARG G:43 , GLU H:4 , ARG I:43 , GLU J:4 , HOH J:166 , HOH J:216 , HOH J:249 , ARG K:43 , GLU L:4 , HOH L:123	BINDING SITE FOR RESIDUE PO4 J 71
8	AC8	SOFTWARE	PRO H:1 , ILE H:37 , ARG K:8 , ARG K:11	BINDING SITE FOR RESIDUE ACT K 76

(no "SS Bond" information available for 3EJ3)

Asymmetric Unit

No.	Residues
1	Gly C:63	-	Asn C:64
2	Val G:61	-	Pro G:62
3	Pro I:62	-	Gly I:63
4	Gly I:63	-	Asn I:64
5	Thr J:9	-	Gly J:10
6	His J:57	-	Gly J:58

(no "SAP(SNP)/Variant" information available for 3EJ3)

(no "PROSITE Motif" information available for 3EJ3)

(no "Exon" information available for 3EJ3)

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:62
 aligned with Q9EV85_PSEPV | Q9EV85 from UniProtKB/TrEMBL  Length:76

    Alignment length:62
                                    11        21        31        41        51        61  
          Q9EV85_PSEPV    2 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 63
               SCOP domains d3ej3a_ A: automated matches                                   SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.eee..ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  3ej3 A  1 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 62
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:61
 aligned with Q9EV84_PSEPV | Q9EV84 from UniProtKB/TrEMBL  Length:71

    Alignment length:61
                                    11        21        31        41        51        61 
          Q9EV84_PSEPV    2 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHGEAA 62
               SCOP domains d3ej3b_ B: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.ee...ee..ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  3ej3 B  1 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHGEAA 61
                                    10        20        30        40        50        60

Chain C from PDB  Type:PROTEIN  Length:64
 aligned with Q9EV85_PSEPV | Q9EV85 from UniProtKB/TrEMBL  Length:76

    Alignment length:64
                                    11        21        31        41        51        61    
          Q9EV85_PSEPV    2 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVPGN 65
               SCOP domains d3ej3c_ C: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.eee..ee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  3ej3 C  1 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVPGN 64
                                    10        20        30        40        50        60

Chain D from PDB  Type:PROTEIN  Length:57
 aligned with Q9EV84_PSEPV | Q9EV84 from UniProtKB/TrEMBL  Length:71

    Alignment length:57
                                    11        21        31        41        51       
          Q9EV84_PSEPV    2 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIH 58
               SCOP domains d3ej3d_ D: automated matches                              SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  3ej3 D  1 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIH 57
                                    10        20        30        40        50

Chain E from PDB  Type:PROTEIN  Length:62
 aligned with Q9EV85_PSEPV | Q9EV85 from UniProtKB/TrEMBL  Length:76

    Alignment length:62
                                    11        21        31        41        51        61  
          Q9EV85_PSEPV    2 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 63
               SCOP domains d3ej3e_ E: automated matches                                   SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.eee..ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  3ej3 E  1 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 62
                                    10        20        30        40        50        60

Chain F from PDB  Type:PROTEIN  Length:58
 aligned with Q9EV84_PSEPV | Q9EV84 from UniProtKB/TrEMBL  Length:71

    Alignment length:58
                                    11        21        31        41        51        
          Q9EV84_PSEPV    2 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHG 59
               SCOP domains d3ej3f_ F: automated matches                               SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  3ej3 F  1 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHG 58
                                    10        20        30        40        50

Chain G from PDB  Type:PROTEIN  Length:62
 aligned with Q9EV85_PSEPV | Q9EV85 from UniProtKB/TrEMBL  Length:76

    Alignment length:62
                                    11        21        31        41        51        61  
          Q9EV85_PSEPV    2 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 63
               SCOP domains d3ej3g_ G: automated matches                                   SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.eee..ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  3ej3 G  1 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 62
                                    10        20        30        40        50        60

Chain H from PDB  Type:PROTEIN  Length:59
 aligned with Q9EV84_PSEPV | Q9EV84 from UniProtKB/TrEMBL  Length:71

    Alignment length:59
                                    11        21        31        41        51         
          Q9EV84_PSEPV    2 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHGE 60
               SCOP domains d3ej3h_ H: automated matches                                SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.ee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  3ej3 H  1 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHGE 59
                                    10        20        30        40        50

Chain I from PDB  Type:PROTEIN  Length:64
 aligned with Q9EV85_PSEPV | Q9EV85 from UniProtKB/TrEMBL  Length:76

    Alignment length:64
                                    11        21        31        41        51        61    
          Q9EV85_PSEPV    2 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVPGN 65
               SCOP domains d3ej3i_ I: automated matches                                     SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.eee..ee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                  3ej3 I  1 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVPGN 64
                                    10        20        30        40        50        60

Chain J from PDB  Type:PROTEIN  Length:58
 aligned with Q9EV84_PSEPV | Q9EV84 from UniProtKB/TrEMBL  Length:71

    Alignment length:58
                                    11        21        31        41        51        
          Q9EV84_PSEPV    2 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHG 59
               SCOP domains d3ej3j_ J: automated matches                               SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.ee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  3ej3 J  1 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHG 58
                                    10        20        30        40        50

Chain K from PDB  Type:PROTEIN  Length:62
 aligned with Q9EV85_PSEPV | Q9EV85 from UniProtKB/TrEMBL  Length:76

    Alignment length:62
                                    11        21        31        41        51        61  
          Q9EV85_PSEPV    2 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 63
               SCOP domains d3ej3k_ K: automated matches                                   SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.eee..ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  3ej3 K  1 PMISCDMRYGRTDEQKRALSAGLLRVISEATGEPRENIFFVIREGSGINFVEHGEHLPDYVP 62
                                    10        20        30        40        50        60

Chain L from PDB  Type:PROTEIN  Length:60
 aligned with Q9EV84_PSEPV | Q9EV84 from UniProtKB/TrEMBL  Length:71

    Alignment length:60
                                    11        21        31        41        51        61
          Q9EV84_PSEPV    2 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHGEA 61
               SCOP domains d3ej3l_ L: automated matches                                 SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeehhh.ee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  3ej3 L  1 PFIECHIATGLSVARKQQLIRDVIDVTNKSIGSDPKIINVLLVEHAEANMSISGRIHGEA 60
                                    10        20        30        40        50        60

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) (23004)

Fold: Tautomerase/MIF (104)

Superfamily: Tautomerase/MIF (104)

Family: 4-oxalocrotonate tautomerase-like (14)

Protein domain: automated matches (3)

Pseudomonas pavonaceae [TaxId: 47881] (3)

1a	d3ej3a_	A:
1b	d3ej3e_	E:
1c	d3ej3f_	F:
1d	d3ej3g_	G:
1e	d3ej3h_	H:
1f	d3ej3i_	I:
1g	d3ej3j_	J:
1h	d3ej3k_	K:
1i	d3ej3l_	L:
1j	d3ej3b_	B:
1k	d3ej3c_	C:
1l	d3ej3d_	D:

(no "CATH Domain" information available for 3EJ3)

(no "Pfam Domain" information available for 3EJ3)

Asymmetric Unit(hide GO term definitions)

Chain A,C,E,G,I,K (Q9EV85_PSEPV | Q9EV85)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.

Chain B,D,F,H,J,L (Q9EV84_PSEPV | Q9EV84)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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	Cis Peptide Bonds
		Gly C:63 - Asn C:64	[ RasMol ]
		Gly I:63 - Asn I:64	[ RasMol ]
		His J:57 - Gly J:58	[ RasMol ]
		Pro I:62 - Gly I:63	[ RasMol ]
		Thr J:9 - Gly J:10	[ RasMol ]
		Val G:61 - Pro G:62	[ RasMol ]

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	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	3ej3
		Family and Domain Information	:	ProDom \| SYSTERS
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	Q9EV84_PSEPV \| Q9EV84
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	Q9EV85_PSEPV \| Q9EV85
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	Q9EV84_PSEPV \| Q9EV84
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	Q9EV85_PSEPV \| Q9EV85
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UniProtKB/TrEMBL
	Q9EV84_PSEPV \| Q9EV84	:	1s0y 3ej7 3ej9
	Q9EV85_PSEPV \| Q9EV85	:	1s0y 3ej7 3ej9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 12)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 4)

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