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Asym./Biol. Unit (Jmol Viewer)

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Title :   LINB (HALOALKANE DEHALOGENASE) FROM SPHINGOMONAS PAUCIMOBILIS UT26 AT ATOMIC RESOLUTION

Authors :   A. J. Oakley, J. Damborsky, M. C. Wilce

Date :   27 Aug 02 (Deposition) - 27 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.95

Chains :   Asym./Biol. Unit : A

Keywords :   Linb, Hydrolase, Haloalkane Dehalogenase, 1, 3, 4, 6- Tetrachloro-1, 4-Cyclohexadiene Dehalogenase, Gamma- Hexachlorocyclohexane Degradation, Alpha/Beta-Hydrolase, Ultra High Resolution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Oakley, M. Klvana, M. Otyepka, Y. Nagata, M. C. Wilce, J. Damborsky
Crystal Structure Of Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis Ut26 At 0. 95 A Resolution: Dynamics Of Catalytic Residues.
Biochemistry V. 43 870 2004
PubMed-ID: 14744129 | Reference-DOI: 10.1021/BI034748G
(for further references see the PDB file header)

Molecule 1 - 1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE
	Chains	:	A
	EC Number	:	3.8.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAQN
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LINB
	Organism Scientific	:	SPHINGOMONAS PAUCIMOBILIS
	Organism Taxid	:	13689
	Strain	:	UT26
	Synonym	:	HALOALKANE DEHALOGENASE, 1,4- TCDN CHLOROHYDROLASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MG	3	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:3013 , HOH A:3019 , HOH A:3029 , HOH A:3032 , HOH A:3038 , HOH A:3064	BINDING SITE FOR RESIDUE MG A 2001
2	AC2	SOFTWARE	HOH A:3039 , HOH A:3114 , HOH A:3115 , HOH A:3116 , HOH A:3143 , HOH A:3173	BINDING SITE FOR RESIDUE MG A 2002
3	AC3	SOFTWARE	HOH A:3075 , HOH A:3083 , HOH A:3086 , HOH A:3108 , HOH A:3118 , HOH A:3138	BINDING SITE FOR RESIDUE MG A 2003
4	AC4	SOFTWARE	ASN A:38 , TRP A:109 , PHE A:169 , PRO A:208	BINDING SITE FOR RESIDUE CL A 2004
5	AC5	SOFTWARE	THR A:216 , ALA A:218 , HOH A:3216 , HOH A:3436	BINDING SITE FOR RESIDUE CL A 2005

(no "SS Bond" information available for 1MJ5)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:38	-	Pro A:39
2	Asp A:73	-	Pro A:74
3	Thr A:216	-	Pro A:217
4	Glu A:244	-	Pro A:245

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LINB_SPHPI_001 *	A	81	T	LINB_SPHPI	---	---	A	A	81	T
2	UniProt	VAR_LINB_SPHPI_002 *	A	112	V	LINB_SPHPI	---	---	A	A	112	V
3	UniProt	VAR_LINB_SPHPI_003 *	I	138	L	LINB_SPHPI	---	---	A	I	138	L
4	UniProt	VAR_LINB_SPHPI_004 *	A	247	H	LINB_SPHPI	---	---	A	A	247	H
5	UniProt	VAR_LINB_SPHPI_005 *	M	253	I	LINB_SPHPI	---	---	A	M	253	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1MJ5)

(no "Exon" information available for 1MJ5)

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:298
 aligned with LINB_SPHPI | P51698 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:298
                                                                                                                                                                                                                                                                                                                                296   
                                    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       261       271       281       291    |   
           LINB_SPHPI     2 SLGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA---   -
               SCOP domains d1mj5a_ A: Haloalkane dehalogenase                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1mj5A00 A:2-299  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..eeeeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------T------------------------------V-------------------------L------------------------------------------------------------------------------------------------------------H-----I---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mj5 A   2 SLGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPAHHH 299
                                    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       261       271       281       291

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: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Haloalkane dehalogenase (50)

Protein domain: Haloalkane dehalogenase (32)

Sphingomonas paucimobilis, UT26, LinB [TaxId: 13689] (12)

d1mj5a_

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

Sphingomonas paucimobilis. Organism_taxid: 13689. Strain: ut26. (1)

1mj5A00

A:2-299

(no "Pfam Domain" information available for 1MJ5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LINB_SPHPI | P51698)

molecular function
	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:0018786	haloalkane dehalogenase activity	Catalysis of the reaction: 1-haloalkane + H2O = a primary alcohol + halide.
	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:0009636	response to toxic substance	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 toxic stimulus.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn A:38 - Pro A:39	[ RasMol ]
		Asp A:73 - Pro A:74	[ RasMol ]
		Glu A:244 - Pro A:245	[ RasMol ]
		Thr A:216 - Pro A:217	[ RasMol ]

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	1mj5
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	3.8.1.5
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UniProtKB/Swiss-Prot
	LINB_SPHPI \| P51698	:	1cv2 1d07 1g42 1g4h 1g5f 1iz7 1iz8 1k5p 1k63 1k6e 2bfn 4wdq

1cv2	FIRST DESCRIPTION OF LINB
1g42	LINB COMPLEXED WITH 1,2-DICHLOROPROPANE
1g4h	LINB COMPLEXED WITH BUTAN-1-OL
1g5f	LINB COMPLEXED WITH 1,2-DICHLOROETHANE

Description

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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