1PDZ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   X-RAY STRUCTURE AND CATALYTIC MECHANISM OF LOBSTER ENOLASE

Authors :   J. Janin, S. Duquerroy, C. Camus, G. Le Bras

Date :   05 Jun 95 (Deposition) - 14 Nov 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Lyase (Carbon-Oxygen) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Duquerroy, C. Camus, J. Janin
X-Ray Structure And Catalytic Mechanism Of Lobster Enolase.
Biochemistry V. 34 12513 1995
PubMed-ID: 7547999 | Reference-DOI: 10.1021/BI00039A005
(for further references see the PDB file header)

Molecule 1 - ENOLASE
	Chains	:	A
	EC Number	:	4.2.1.11
	Organ	:	TAIL
	Organism Common	:	EUROPEAN LOBSTER
	Organism Scientific	:	HOMARUS GAMMARUS
	Organism Taxid	:	6707
	Synonym	:	2-PHOSPHO-D-GLYCERATE DEHYDRATASE
	Tissue	:	TAIL MUSCLE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	MN	1	Ligand/Ion	MANGANESE (II) ION
3	PGA	1	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	PGA	2	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:36 , HIS A:157 , GLU A:209 , LYS A:344 , ARG A:373 , SER A:374 , HOH A:441 , HOH A:444 , HOH A:569	BINDING SITE FOR RESIDUE PGA A 439
2	AC2	SOFTWARE	ASP A:244 , GLU A:294 , ASP A:319 , HOH A:441 , HOH A:442 , HOH A:443	BINDING SITE FOR RESIDUE MN A 440

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

(no "Cis Peptide Bond" information available for 1PDZ)

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOLASE	PS00164	Enolase signature.	ENO_HOMGA	341-354	1	A:341-354

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOLASE	PS00164	Enolase signature.	ENO_HOMGA	341-354	2	A:341-354

(no "Exon" information available for 1PDZ)

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:434
 aligned with ENO_HOMGA | P56252 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:434
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    
            ENO_HOMGA     - -SITKVFARTIFDSRGNPTVEVDLYTSKGLFRAAVPSGASTGVHEALEMRDGDKSKYHGKSVFNAVKNVNDVIVPEIIKSGLKVTQQKECDEFMCKLDGTENKSSLGANAILGVSLAICKAGAAELGIPLYRHIANLANYDEVILPVPAFNVINGGSHAGNKLAMQEFMILPTGATSFTEAMRMGTEVYHHLKAVIKARFGLDATAVGDEGGFAPNILNNKDALDLIQEAIKKAGYTGKIEIGMDVAASEFYKQNNIYDLDFKTANNDGSQKISGDQLRDMYMEFCKDFPIVSIEDPFDQDDWETWSKMTSGTTIQIVGDDLTVTNPKRITTAVEKKACKCLLLKVNQIGSVTESIDAHLLAKKNGWGTMVSHRSGETEDCFIADLVVGLCTGQIKTGAPCRSERLAKYNQILRIEEELGSGAKFAGKNFRAPS 433
               SCOP domains -d1pdza2 A:1-139 Enolase                                                                                                                    d1pdza1 A:140-433 Enolase                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1pdzA01 A:1-126 Enolase-like, N-terminal domain                                                                               1pdzA02 A:127-433 Enolase superfamily                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....eeeeeeeee..eeeeee......................hhh...hhhhhhhhh.hhhhhhhh......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh....hhhhhhhh...........eeeeee............eeeee......hhhhhhhhhhhhhhhhhhhhhhh.hhhh..............hhhhhhhhhhhhhhh......eeeee..............hhh............hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhh...eee........hhhhhhhhh.....eeee.hhhh..hhhhhhhhhhhhhh..eeee..........hhhhhhhh.............hhhhhhhhhhhhhhhhhhhh....hhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ENOLASE       ------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pdz A   0 xSITKVFARTIFDSRGNPTVEVDLYTSKGLFRAAVPSGASTGVHEALEMRDGDKSKYHGKSVFNAVKNVNDVIVPEIIKSGLKVTQQKECDEFMCKLDGTENKSSLGANAILGVSLAICKAGAAELGIPLYRHIANLANYDEVILPVPAFNVINGGSHAGNKLAMQEFMILPTGATSFTEAMRMGTEVYHHLKAVIKARFGLDATAVGDEGGFAPNILNNKDALDLIQEAIKKAGYTGKIEIGMDVAASEFYKQNNIYDLDFKTANNDGSQKISGDQLRDMYMEFCKDFPIVSIEDPFDQDDWETWSKMTSGTTIQIVGDDLTVTNPKRITTAVEKKACKCLLLKVNQIGSVTESIDAHLLAKKNGWGTMVSHRSGETEDCFIADLVVGLCTGQIKTGAPCRSERLAKYNQILRIEEELGSGAKFAGKNFRAPS 433
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                            0-ACE

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: Enolase-like, N-terminal domain (130)

European lobster (Homarus gammarus) (2)

1pdzA01

A:1-126

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Enolase superfamily (142)

European lobster (Homarus gammarus) (2)

1pdzA02

A:127-433

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

Asymmetric Unit(hide GO term definitions)

Chain A (ENO_HOMGA | P56252)

molecular function
	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.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004634	phosphopyruvate hydratase activity	Catalysis of the reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O.
biological process
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000015	phosphopyruvate hydratase complex	A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water.

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
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PGA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pdz)

Biological Unit
	Complete Structure
		Biological Unit 1	[ 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 ](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
	1pdz
		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
	ENO_HOMGA \| P56252
		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)
	4.2.1.11
		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
	ENO_HOMGA \| P56252
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ENO_HOMGA \| P56252	:	1pdy

(no "Related Entries Specified in the PDB File" available for 1PDZ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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