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Asym./Biol. Unit (Jmol Viewer)

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Title :   RE-REFINEMENT OF THE STRUCTURE OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,3-PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, AT 2.0A RESOLUTION

Authors :   V. A. Streltsov

Date :   30 Sep 02 (Deposition) - 16 Oct 02 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Dehalogenase, Lindane, Biodegradation, Alpha/Beta-Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. A. Streltsov, Z. Prokop, J. Damborsky, Y. Nagata, A. Oakley, M. C. J. Wilce
Haloalkane Dehalogenase Linb From Sphingomonas Paucimobilis Ut26: X-Ray Crystallographic Studies Of Dehalogenation Of Brominated Substrates
Biochemistry V. 42 10104 2003
PubMed-ID: 12939138 | Reference-DOI: 10.1021/BI027280A
(for further references see the PDB file header)

Molecule 1 - HALOALKANE DEHALOGENASE, LINB
	Chains	:	A
	EC Number	:	3.8.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMYLB1
	Expression System Strain	:	HB101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SPHINGOMONAS PAUCIMOBILIS
	Organism Taxid	:	13689
	Strain	:	UT26
	Synonym	:	1,3,4,6-TETRACHLORO-1,4-CYCLOHEXADIENE HYDROLASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	BR	1	Ligand/Ion	BROMIDE ION
2	CA	3	Ligand/Ion	CALCIUM ION
3	PDO	1	Ligand/Ion	1,3-PROPANDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:38 , TRP A:109 , PHE A:169 , PRO A:208	BINDING SITE FOR RESIDUE BR A 1
2	AC2	SOFTWARE	GLN A:165 , ASP A:166 , PRO A:175 , ILE A:178 , HOH A:1007 , HOH A:1028	BINDING SITE FOR RESIDUE CA A 2002
3	AC3	SOFTWARE	HOH A:1231 , HOH A:1236 , HOH A:1271 , HOH A:1272	BINDING SITE FOR RESIDUE CA A 2003
4	AC4	SOFTWARE	ASP A:149 , GLN A:152 , GLU A:233 , HOH A:1003 , HOH A:1117 , HOH A:1276	BINDING SITE FOR RESIDUE CA A 2004
5	AC5	SOFTWARE	ASP A:108 , PHE A:143 , PRO A:144 , PHE A:151 , LEU A:177 , ALA A:247 , HIS A:272 , HOH A:1274	BINDING SITE FOR RESIDUE PDO A 2001

(no "SS Bond" information available for 1IZ8)

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 1IZ8)

(no "Exon" information available for 1IZ8)

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:294
 aligned with LINB_SPHPI | P51698 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:294
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292    
           LINB_SPHPI     3 LGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA 296
               SCOP domains d1iz8a_ A: Haloalkane dehalogenase                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1iz8A00 A:3-296  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee......eeeeee....eeeee.....hhhhhh.hhhhhh...eeeee...................hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------T------------------------------V-------------------------L------------------------------------------------------------------------------------------------------------H-----I------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1iz8 A   3 LGAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA 296
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292

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)

d1iz8a_

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. (5)

1iz8A00

A:3-296

(no "Pfam Domain" information available for 1IZ8)

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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Access by PDB/NDB ID
	1iz8
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	LINB_SPHPI \| P51698
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

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	3.8.1.-
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Age Related Information	:	GenAge

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	LINB_SPHPI \| P51698
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UniProtKB/Swiss-Prot
	LINB_SPHPI \| P51698	:	1cv2 1d07 1g42 1g4h 1g5f 1iz7 1k5p 1k63 1k6e 1mj5 2bfn 4wdq

1cv2	1CV2 CONTAINS THE SAME PROTEIN, DIFFERENT REFINEMENT MODEL
1d07	1D07 CONTAINS THE SAME PROTEIN COMPLEXED WITH 1,3- PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, DIFFERENT REFINEMENT MODEL
1iz7	1IZ7 CONTAINS PROTEIN LINB, STRUCTURE RE-REFINED FROM 1CV2 RELATED ID: R1D07SF RELATED DB: PDB THIS ENTRY 1IZ8 REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1D07SF.
1k5p	1K5P CONTAINS THE SAME PROTEIN, DIFFERENT CRYSTAL STRUCTURE
1k63	1K63 CONTAINS THE SAME PROTEIN COMPLEXED WITH 2-BROMO-2- PROPENE-1-OL
1k6e	1K6E CONTAINS THE SAME PROTEIN COMPLEX WITH 1,2- PROPANEDIOL, A PRODUCT OF DEHALOGENATION OF 1,2- DIBROMOPROPANE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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