2AHC - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CHORISMATE LYASE WITH INHIBITOR VANILATE

Authors :   D. T. Gallagher, N. N. Smith

Date :   27 Jul 05 (Deposition) - 31 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Unique Fold, Ubiquinone Pathway, 123654 Antiparallel Sheet, Internal Active Site, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. N. Smith, A. E. Roitberg, E. Rivera, A. Howard, M. J. Holden, M. Mayhew, S. Kaistha, D. T. Gallagher
Structural Analysis Of Ligand Binding And Catalysis In Chorismate Lyase
Arch. Biochem. Biophys. V. 445 72 2006
PubMed-ID: 16343413 | Reference-DOI: 10.1016/J.ABB.2005.10.026

Molecule 1 - CHORISMATE LYASE
	Chains	:	A, B, C, D
	EC Number	:	4.1.3.40
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSE380
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	UBIC
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	VNL	4	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	VNL	1	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	VNL	1	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	VNL	1	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	VNL	1	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:34 , ARG A:76 , ILE A:78 , LEU A:114 , LEU A:153 , GLU A:155 , HOH A:201	BINDING SITE FOR RESIDUE VNL A 166
2	AC2	SOFTWARE	MET B:34 , THR B:35 , ARG B:76 , ILE B:78 , THR B:92 , PRO B:113 , LEU B:114 , THR B:154 , GLU B:155 , HOH B:301	BINDING SITE FOR RESIDUE VNL B 266
3	AC3	SOFTWARE	ARG C:76 , PRO C:113 , LEU C:114 , THR C:154 , GLU C:155	BINDING SITE FOR RESIDUE VNL C 366
4	AC4	SOFTWARE	MET D:34 , THR D:35 , ARG D:76 , ILE D:78 , LEU D:80 , THR D:92 , PRO D:113 , LEU D:114 , THR D:154 , GLU D:155 , HOH D:501	BINDING SITE FOR RESIDUE VNL D 466

(no "SS Bond" information available for 2AHC)

(no "Cis Peptide Bond" information available for 2AHC)

(no "SAP(SNP)/Variant" information available for 2AHC)

(no "PROSITE Motif" information available for 2AHC)

(no "Exon" information available for 2AHC)

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:164
 aligned with UBIC_ECOLI | P26602 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           UBIC_ECOLI     2 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 165
               SCOP domains d2ahca_ A: Chorismate lyase                                                                                                                                          SCOP domains
               CATH domains 2ahcA00 A:1-164 Chorismate lyase                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhee..........hhhhhh...hhhhhhhhh...eeeeeeeeeeehhhhh..hhhhh.....eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhh...............eeeeeeeeeee..eeeeeeeeee..eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahc A   1 SHPALTQLRALRYSKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLSADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with UBIC_ECOLI | P26602 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           UBIC_ECOLI     2 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 165
               SCOP domains d2ahcb_ B: Chorismate lyase                                                                                                                                          SCOP domains
               CATH domains 2ahcB00 B:1-164 Chorismate lyase                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..eee......hhhhhhhhh...hhhhhhhh....eeeeeeeeeeehhhhh..hhhhh.....eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhh...............eeeeeeeeeee..eeeeeeeeee..eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahc B   1 SHPALTQLRALRYSKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLSADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:164
 aligned with UBIC_ECOLI | P26602 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           UBIC_ECOLI     2 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 165
               SCOP domains d2ahcc_ C: Chorismate lyase                                                                                                                                          SCOP domains
               CATH domains 2ahcC00 C:1-164 Chorismate lyase                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.ee....................hhhhhhh....eeeeeeeeeeehhhhh..hhhhh.....eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhh...............eeeeeeeeeee..eeeeeeeeee..eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahc C   1 SHPALTQLRALRYSKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLSADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain D from PDB  Type:PROTEIN  Length:164
 aligned with UBIC_ECOLI | P26602 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           UBIC_ECOLI     2 SHPALTQLRALRYCKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLCADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 165
               SCOP domains d2ahcd_ D: Chorismate lyase                                                                                                                                          SCOP domains
               CATH domains 2ahcD00 D:1-164 Chorismate lyase                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..eee.........hhhhhh...hhhhhhhhh...eeeeeeeeeeehhhhh..hhhhh.....eeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhh...............eeeeeeeeeee..eeeeeeeeee..eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ahc D   1 SHPALTQLRALRYSKEIPALDPQLLDWLLLEDSMTKRFEQQGKTVSVTMIREGFVEQNEIPEELPLLPKESRYWLREILLSADGEPWLAGRTVVPVSTLSGPELALQKLGKTPLGRYLFTSSTLTRDFIEIGRDAGLWGRRSRLRLSGKPLLLTELFLPASPLY 164
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

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: Chorismate lyase-like (23)

Superfamily: Chorismate lyase-like (23)

Family: Chorismate lyase (7)

Protein domain: Chorismate lyase (7)

Escherichia coli [TaxId: 562] (7)

1a	d2ahca_	A:
1b	d2ahcd_	D:
1c	d2ahcb_	B:
1d	d2ahcc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Chorismate lyase (20)

Homologous Superfamily: Chorismate lyase (20)

Escherichia coli. Organism_taxid: 562. (5)

1a	2ahcA00	A:1-164
1b	2ahcB00	B:1-164
1c	2ahcC00	C:1-164
1d	2ahcD00	D:1-164

(no "Pfam Domain" information available for 2AHC)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (UBIC_ECOLI | P26602)

molecular function
	GO:0008813	chorismate lyase activity	Catalysis of the reaction: chorismate = 4-hydroxybenzoate + pyruvate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0042866	pyruvate biosynthetic process	The chemical reactions and pathways resulting in the formation of pyruvate, 2-oxopropanoate.
	GO:0006744	ubiquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric 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
		VNL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ahc)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	2ahc
		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
	UBIC_ECOLI \| P26602
		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)
	4.1.3.40
		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
	UBIC_ECOLI \| P26602
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	UBIC_ECOLI \| P26602	:	1fw9 1g1b 1g81 1jd3 1tt8 1xlr

1tt8	PRODUCT COMPLEX
1xlr	VAN COMPLEX WITH G90A MUTATION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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