1QQ7 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF L-2-HALOACID DEHALOGENASE FROM XANTHOBACTER AUTOTROPHICUS WITH CHLOROPROPIONIC ACID COVALENTLY BOUND

Authors :   I. S. Ridder, H. J. Rozeboom, K. H. Kalk, B. W. Dijkstra

Date :   11 Jun 99 (Deposition) - 25 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   L-2-Haloacid Dehalogenase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. S. Ridder, H. J. Rozeboom, K. H. Kalk, B. W. Dijkstra
Crystal Structures Of Intermediates In The Dehalogenation Of Haloalkanoates By L-2-Haloacid Dehalogenase.
J. Biol. Chem. V. 274 30672 1999
PubMed-ID: 10521454 | Reference-DOI: 10.1074/JBC.274.43.30672
(for further references see the PDB file header)

Molecule 1 - PROTEIN (L-2-HALOACID DEHALOGENASE)
	Chains	:	A, B
	EC Number	:	3.8.1.2
	Organism Scientific	:	XANTHOBACTER AUTOTROPHICUS
	Organism Taxid	:	280
	Other Details	:	2-CHLOROPROPIONIC ACID MOIETY COVALENTLY BOUND TO ASP 8 IN ACTIVE SITES OF BOTH CHAINS
	Strain	:	GJ10

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ASB	2	Mod. Amino Acid	ASPARTIC ACID-4-CARBOXYMETHYL ESTER
2	CL	2	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASB A:8 , TYR A:10 , ARG A:39 , ASN A:115	BINDING SITE FOR RESIDUE CL A 1401
2	AC2	SOFTWARE	ASB B:8 , ARG B:39 , ASN B:115	BINDING SITE FOR RESIDUE CL B 1402

(no "SS Bond" information available for 1QQ7)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:106	-	Pro A:107
2	Lys A:147	-	Pro A:148
3	Lys B:147	-	Pro B:148

(no "SAP(SNP)/Variant" information available for 1QQ7)

(no "PROSITE Motif" information available for 1QQ7)

(no "Exon" information available for 1QQ7)

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:245
 aligned with HAD_XANAU | Q60099 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
            HAD_XANAU     1 MIKAVVFDAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
               SCOP domains d1qq7a_ A: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                                             SCOP domains
               CATH domains 1qq7A01        1qq7A02 A:16-90 Putative phosphatase; domain 2                             1qq7A01 A:1-15,A:91-241  [code=3.40.50.1000, no name defined]                                                                                          ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhh..eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....hhhhhhhhhhh..........eee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qq7 A   1 MIKAVVFdAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
                                   |10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                                   8-ASB

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with HAD_XANAU | Q60099 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
            HAD_XANAU     1 MIKAVVFDAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
               SCOP domains d1qq7b_ B: L-2-Haloacid dehalogenase, HAD                                                                                                                                                                                                             SCOP domains
               CATH domains 1qq7B01        1qq7B02 B:16-90 Putative phosphatase; domain 2                             1qq7B01 B:1-15,B:91-241  [code=3.40.50.1000, no name defined]                                                                                          ---- CATH domains
           Pfam domains (1) -Hydrolase-1qq7B01 B:2-184                                                                                                                                                              ------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -Hydrolase-1qq7B02 B:2-184                                                                                                                                                              ------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhh....eeeeee..hhhhhhhhhhhh.hhhhh.eeee.hhhh....hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh.eeeee...hhhhhhhhh.....hhhhhhhhhhh..........eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qq7 B   1 MIKAVVFdAYGTLFDVQSVADATERAYPGRGEYITQVWRQKQLEYSWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQAYNRLTPYPDAAQCLAELAPLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQEALARELVSGTIAPLTMFKALRMREETYAEAPDFVVPALGDLPRLVRGMA 245
                                   |10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
                                   8-ASB

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: HAD-like (349)

Superfamily: HAD-like (349)

Family: HAD-related (11)

Protein domain: L-2-Haloacid dehalogenase, HAD (8)

Xanthobacter autotrophicus [TaxId: 280] (4)

1a	d1qq7a_	A:
1b	d1qq7b_	B:

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=3.40.50.1000, no name defined] (211)

Xanthobacter autotrophicus. Organism_taxid: 280. Strain: gj10 (4)

1a	1qq7A01	A:1-15,A:91-241
1b	1qq7B01	B:1-15,B:91-241

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: Putative phosphatase; domain 2 (65)

Xanthobacter autotrophicus. Organism_taxid: 280. Strain: gj10 (4)

2a	1qq7A02	A:16-90
2b	1qq7B02	B:16-90

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Hydrolase (64)

Xanthobacter autotrophicus (3)

1a	Hydrolase-1qq7B01	B:2-184
1b	Hydrolase-1qq7B02	B:2-184

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HAD_XANAU | Q60099)

molecular function
	GO:0018784	(S)-2-haloacid dehalogenase activity	Catalysis of the reaction: (S)-2-haloacid + H2O = (R)-2-hydroxyacid + 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.
	GO:0019120	hydrolase activity, acting on acid halide bonds, in C-halide compounds	Catalysis of the hydrolysis of any acid halide bond in substances containing halogen atoms in organic linkage.
biological process
	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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ASB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:106 - Pro A:107	[ RasMol ]
		Lys A:147 - Pro A:148	[ RasMol ]
		Lys B:147 - Pro B:148	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1qq7
		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
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HAD_XANAU \| Q60099
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.8.1.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HAD_XANAU \| Q60099
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HAD_XANAU \| Q60099	:	1aq6 1qq5 1qq6

1aq6	FIRST NATIVE STRUCTURE OF THE L-2-HALOACID DEHALOGENASE ENZYME
1qq5
1qq6

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File