1THG - JenaLib

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Title :   1.8 ANGSTROMS REFINED STRUCTURE OF THE LIPASE FROM GEOTRICHUM CANDIDUM

Authors :   J. D. Schrag, M. Cygler

Date :   28 Jul 92 (Deposition) - 31 Oct 93 (Release) - 13 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase(Carboxylic Esterase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Schrag, M. Cygler
1. 8 A Refined Structure Of The Lipase From Geotrichum Candidum.
J. Mol. Biol. V. 230 575 1993
PubMed-ID: 8464065 | Reference-DOI: 10.1006/JMBI.1993.1171
(for further references see the PDB file header)

Molecule 1 - LIPASE 2
	Chains	:	A
	EC Number	:	3.1.1.3
	Engineered	:	YES
	Gene	:	LIP2
	Organism Common	:	OOSPORA LACTIS
	Organism Scientific	:	GEOTRICHUM CANDIDUM
	Organism Taxid	:	1173061
	Strain	:	ATCC 34614
	Synonym	:	GCL II, LIPASE II

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:364 , HIS A:370 , LYS A:373 , TRP A:374 , NAG A:991	BINDING SITE FOR RESIDUE NAG A 990
2	AC2	SOFTWARE	PHE A:310 , LYS A:373 , TYR A:377 , HOH A:719 , NAG A:990	BINDING SITE FOR RESIDUE NAG A 991
3	AC3	SOFTWARE	ASN A:283 , HOH A:686 , HOH A:816	BINDING SITE FOR RESIDUE NAG A 994
4	AC4	SOFTWARE	THR A:4 , VAL A:6 , ALA A:282 , HOH A:649 , HOH A:678 , HOH A:814	BINDING SITE FOR RESIDUE NDG A 996
5	ACT	AUTHOR	SER A:217 , GLU A:354 , HIS A:463	ACTIVE SITE

Asymmetric/Biological Unit

No.	Residues
1	A:61	-	A:105
2	A:276	-	A:288

Asymmetric/Biological Unit

No.	Residues
1	Ser A:402	-	Pro A:403

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_LIP2_GEOCN_001 *	I	46	V	LIP2_GEOCN	---	---	A	I	27	V
2	UniProt	VAR_LIP2_GEOCN_002 *	I	247	V	LIP2_GEOCN	---	---	A	I	228	V
3	UniProt	VAR_LIP2_GEOCN_003 *	F	355	Y	LIP2_GEOCN	---	---	A	F	336	Y
4	UniProt	VAR_LIP2_GEOCN_004 *	K	391	R	LIP2_GEOCN	---	---	A	K	372	R
5	UniProt	VAR_LIP2_GEOCN_005 *	A	439	S	LIP2_GEOCN	---	---	A	A	420	S
6	UniProt	VAR_LIP2_GEOCN_006 *	N	484	D	LIP2_GEOCN	---	---	A	N	465	D
	* ID not provided by source

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CARBOXYLESTERASE_B_2	PS00941	Carboxylesterases type-B signature 2.	LIP2_GEOCN	122-132	1	A:103-113
1	CARBOXYLESTERASE_B_2	PS00941	Carboxylesterases type-B signature 2.	LIP1_GEOFE	122-132	1	A:103-113
2	CARBOXYLESTERASE_B_1	PS00122	Carboxylesterases type-B serine active site.	LIP2_GEOCN	223-238	1	A:204-219
2	CARBOXYLESTERASE_B_1	PS00122	Carboxylesterases type-B serine active site.	LIP1_GEOFE	223-238	1	A:204-219

(no "Exon" information available for 1THG)

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:544
 aligned with LIP1_GEOFE | P79066 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:544
                                    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       439       449       459       469       479       489       499       509       519       529       539       549       559    
           LIP1_GEOFE    20 QAPTAVLNGNEVISGVLEGKVDTFKGIPFADPPLNDLRFKHPQPFTGSYQGLKANDFSPACMQLDPGNSLTLLDKALGLAKVIPEEFRGPLYDMAKGTVSMNEDCLYLNVFRPAGTKPDAKLPVMVWIYGGAFVYGSSAAYPGNSYVKESINMGQPVVFVSINYRTGPFGFLGGDAITAEGNTNAGLHDQRKGLEWVSDNIANFGGDPDKVMIFGESAGAMSVAHQLIAYGGDNTYNGKKLFHSAILQSGGPLPYHDSSSVGPDISYNRFAQYAGCDTSASANDTLECLRSKSSSVLHDAQNSYDLKDLFGLLPQFLGFGPRPDGNIIPDAAYELFRSGRYAKVPYISGNQEDEGTAFAPVALNATTTPHVKKWLQYIFYDASEASIDRVLSLYPQTLSVGSPFRTGILNALTPQFKRVAAILSDMLFQSPRRVMLSATKDVNRWTYLSTHLHNLVPFLGTFHGNELIFQFNVNIGPANSYLRYFISFANHHDPNVGTNLLQWDQYTDEGKEMLEIHMTDNVMRTDDYRIEGISNFETDVNLYG 563
               SCOP domains d1thga_ A: Type-B carboxylesterase/lipase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -1thgA00 A:2-544  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -COesterase-1thgA01 A:2-531                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ------------- Pfam domains
         Sec.struct. author ...eeee...eeee.eee..eeeeeeee......................eeee...........hhhhhhhhhhhh.......hhhhhhhhhhh...........eeeeeee.........eeeeee...............hhhhhhhhh.....eeeee............hhhhhh....hhhhhhhhhhhhhhhh.........eeeeeee.hhhhhhhhhh................eeeee.................hhhhhhhhh.......hhhhhhhhhh..hhhhhhhhhhhhhhh.......................hhhhhh.......eeeeeee....hhhhh.......hhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.................hhhhh......hhhhhhhhhhhhhh.....................eeee....eeeee....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-----------------------------------------------------------------------------------------------------------Y-----------------------------------R-----------------------------------------------S--------------------------------------------D------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------CARBOXYLEST----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYLESTERASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1thg A   1 xAPTAVLNGNEVISGVLEGKVDTFKGIPFADPPLNDLRFKHPQPFTGSYQGLKANDFSPACMQLDPGNSLTLLDKALGLAKVIPEEFRGPLYDMAKGTVSMNEDCLYLNVFRPAGTKPDAKLPVMVWIYGGAFVYGSSAAYPGNSYVKESINMGQPVVFVSINYRTGPFGFLGGDAITAEGNTNAGLHDQRKGLEWVSDNIANFGGDPDKVMIFGESAGAMSVAHQLIAYGGDNTYNGKKLFHSAILQSGGPLPYHDSSSVGPDISYNRFAQYAGCDTSASANDTLECLRSKSSSVLHDAQNSYDLKDLFGLLPQFLGFGPRPDGNIIPDAAYELFRSGRYAKVPYISGNQEDEGTAFAPVALNATTTPHVKKWLQYIFYDASEASIDRVLSLYPQTLSVGSPFRTGILNALTPQFKRVAAILSDMLFQSPRRVMLSATKDVNRWTYLSTHLHNLVPFLGTFHGNELIFQFNVNIGPANSYLRYFISFANHHDPNVGTNLLQWDQYTDEGKEMLEIHMTDNVMRTDDYRIEGISNFETDVNLYG 544
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540    
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                            1-PCA

Chain A from PDB  Type:PROTEIN  Length:544
 aligned with LIP2_GEOCN | P22394 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:544
                                    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       439       449       459       469       479       489       499       509       519       529       539       549       559    
           LIP2_GEOCN    20 QAPRPSLNGNEVISGVLEGKVDTFKGIPFADPPLNDLRFKHPQPFTGSYQGLKANDFSPACMQLDPGNSLTLLDKALGLAKVIPEEFRGPLYDMAKGTVSMNEDCLYLNVFRPAGTKPDAKLPVMVWIYGGAFVYGSSAAYPGNSYVKESINMGQPVVFVSINYRTGPFGFLGGDAITAEGNTNAGLHDQRKGLEWVSDNIANFGGDPDKVMIFGESAGAMSVAHQLIAYGGDNTYNGKKLFHSAILQSGGPLPYHDSSSVGPDISYNRFAQYAGCDTSASANDTLECLRSKSSSVLHDAQNSYDLKDLFGLLPQFLGFGPRPDGNIIPDAAYELFRSGRYAKVPYISGNQEDEGTAFAPVALNATTTPHVKKWLQYIFYDASEASIDRVLSLYPQTLSVGSPFRTGILNALTPQFKRVAAILSDMLFQSPRRVMLSATKDVNRWTYLSTHLHNLVPFLGTFHGNELIFQFNVNIGPANSYLRYFISFANHHDPNVGTNLLQWDQYTDEGKEMLEIHMTDNVMRTDDYRIEGISNFETDVNLYG 563
               SCOP domains d1thga_ A: Type-B carboxylesterase/lipase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -1thgA00 A:2-544  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains -COesterase-1thgA01 A:2-531                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        ------------- Pfam domains
         Sec.struct. author ...eeee...eeee.eee..eeeeeeee......................eeee...........hhhhhhhhhhhh.......hhhhhhhhhhh...........eeeeeee.........eeeeee...............hhhhhhhhh.....eeeee............hhhhhh....hhhhhhhhhhhhhhhh.........eeeeeee.hhhhhhhhhh................eeeee.................hhhhhhhhh.......hhhhhhhhhh..hhhhhhhhhhhhhhh.......................hhhhhh.......eeeeeee....hhhhh.......hhhhhhhhhhh.....hhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee.................hhhhh......hhhhhhhhhhhhhh.....................eeee....eeeee....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V-----------------------------------------------------------------------------------------------------------Y-----------------------------------R-----------------------------------------------S--------------------------------------------D------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------------------------------------------------------CARBOXYLEST----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYLESTERASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1thg A   1 xAPTAVLNGNEVISGVLEGKVDTFKGIPFADPPLNDLRFKHPQPFTGSYQGLKANDFSPACMQLDPGNSLTLLDKALGLAKVIPEEFRGPLYDMAKGTVSMNEDCLYLNVFRPAGTKPDAKLPVMVWIYGGAFVYGSSAAYPGNSYVKESINMGQPVVFVSINYRTGPFGFLGGDAITAEGNTNAGLHDQRKGLEWVSDNIANFGGDPDKVMIFGESAGAMSVAHQLIAYGGDNTYNGKKLFHSAILQSGGPLPYHDSSSVGPDISYNRFAQYAGCDTSASANDTLECLRSKSSSVLHDAQNSYDLKDLFGLLPQFLGFGPRPDGNIIPDAAYELFRSGRYAKVPYISGNQEDEGTAFAPVALNATTTPHVKKWLQYIFYDASEASIDRVLSLYPQTLSVGSPFRTGILNALTPQFKRVAAILSDMLFQSPRRVMLSATKDVNRWTYLSTHLHNLVPFLGTFHGNELIFQFNVNIGPANSYLRYFISFANHHDPNVGTNLLQWDQYTDEGKEMLEIHMTDNVMRTDDYRIEGISNFETDVNLYG 544
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540    
                            1-PCA

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: Fungal lipases (53)

Protein domain: Type-B carboxylesterase/lipase (11)

Fungus (Geotrichum candidum), ATCC 34614 [TaxId: 27317] (1)

d1thga_

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)

Ascomycetes (Galactomyces geotrichum) (1)

1thgA00

A:2-544

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: COesterase (79)

Geotrichum fermentans (Trichosporon fermentans) (1)

COesterase-1thgA01

A:2-531

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (LIP1_GEOFE | P79066)

molecular function
	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:0004806	triglyceride lipase activity	Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
biological process
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A (LIP2_GEOCN | P22394)

molecular function
	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:0004806	triglyceride lipase activity	Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
biological process
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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		Ser A:402 - Pro A:403	[ RasMol ]

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Ligands, Modified Residues, Ions (3, 5)

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