2HIH - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF STAPHYLOCOCCUS HYICUS LIPASE

Authors :   J. J. W. Tiesinga, G. Van Pouderoyen, M. Nardini, B. W. Dijkstra

Date :   29 Jun 06 (Deposition) - 22 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.86

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

Keywords :   Lipase, A1 Phospholipase, Phospholipid Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Tiesinga, G. Van Pouderoyen, M. Nardini, S. Ransac, B. W. Dijkstra
Structural Basis Of Phospholipase Activity Of Staphylococcu Hyicus Lipase.
J. Mol. Biol. V. 371 447 2007
PubMed-ID: 17582438 | Reference-DOI: 10.1016/J.JMB.2007.05.041

Molecule 1 - LIPASE 46 KDA FORM
	Chains	:	A, B
	EC Number	:	3.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PSHT7
	Expression System Strain	:	BL21(DE 3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LIP
	Organism Scientific	:	STAPHYLOCOCCUS HYICUS
	Organism Taxid	:	1284

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:72 , HIS A:92 , HIS A:98 , ASP A:243	BINDING SITE FOR RESIDUE ZN A 601
2	AC2	SOFTWARE	GLY A:290 , ASP A:354 , ASP A:357 , ASP A:362 , ASP A:365	BINDING SITE FOR RESIDUE CA A 603
3	AC3	SOFTWARE	GLU B:72 , HIS B:92 , HIS B:98 , ASP B:243	BINDING SITE FOR RESIDUE ZN B 1601
4	AC4	SOFTWARE	GLY B:290 , ASP B:354 , ASP B:357 , ASP B:362 , ASP B:365	BINDING SITE FOR RESIDUE CA B 1603

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIP_STAHY	363-372	2	A:118-127 B:118-127

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIP_STAHY	363-372	1	A:118-127 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIP_STAHY	363-372	1	- B:118-127

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIP_STAHY	363-372	2	A:118-127 B:118-127

(no "Exon" information available for 2HIH)

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:387
 aligned with LIP_STAHY | P04635 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:387
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       
            LIP_STAHY   252 AVQNPENPKNKDPFVFVHGFTGFVGEVAAKGENHWGGTKANLRNHLRKAGYETYEASVSALASNHERAVELYYYLKGGRVDYGAAHSEKYGHERYGKTYEGVLKDWKPGHPVHFIGHSMGGQTIRLLEHYLRFGDKAEIAYQQQHGGIISELFKGGQDNMVTSITTIATPHNGTHASDDIGNTPTIRNILYSFAQMSSHLGTIDFGMDHWGFKRKDGESLTDYNKRIAESKIWDSEDTGLYDLTREGAEKINQKTELNPNIYYKTYTGVATHETQLGKHIADLGMEFTKILTGNYIGSVDDILWRPNDGLVSEISSQHPSDEKNISVDENSELHKGTWQVMPTMKGWDHSDFIGNDALDTKHSAIELTNFYHSISDYLMRIEKAEST 638
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hihA00 A:7-393  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee......hhhhh............hhhhhhhhh...eeee......hhhhhhhhhhhhhhheeee.hhhhhhhhh...eeeee............eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.....eeeeeee......hhhhhh...hhhhhhhhhhhhhhhhhh......hhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......eeeee.ee.eee.hhh.eee....hhhhhhhhhhhh...hhhhh......hhhhhhh.....eee...........eee...ee....hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------LIPASE_SER-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hih A   7 AVQNPENPKNKDPFVFVHGFTGFVGEVAAKGENYWGGTKANLRNHLRKAGYETYEASVSALASNHERAVELYYYLKGGRVDYGAAHSEKYGHERYGKTYEGVLKDWKPGHPVHFIGHSMGGQTIRLLEHYLRFGDKAEIAYQQQHGGIISELFKGGQDNMVTSITTIATPHNGTHASDDIGNTPTIRNILYSFAQMSSHLGTIDFGMDHWGFKRKDGESLTDYNKRIAESKIWDSEDTGLYDLTREGAEKINQKTELNPNIYYKTYTGVATHETQLGKHIADLGMEFTKILTGNYIGSVDDILWRPNDGLVSEISSQHPSDEKNISVDENSELHKGTWQVMPTMKGWDHSDFIGNDALDTKHSAIELTNFYHSISDYLMRIEKAEST 393
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386

Chain B from PDB  Type:PROTEIN  Length:386
 aligned with LIP_STAHY | P04635 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:386
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631      
            LIP_STAHY   252 AVQNPENPKNKDPFVFVHGFTGFVGEVAAKGENHWGGTKANLRNHLRKAGYETYEASVSALASNHERAVELYYYLKGGRVDYGAAHSEKYGHERYGKTYEGVLKDWKPGHPVHFIGHSMGGQTIRLLEHYLRFGDKAEIAYQQQHGGIISELFKGGQDNMVTSITTIATPHNGTHASDDIGNTPTIRNILYSFAQMSSHLGTIDFGMDHWGFKRKDGESLTDYNKRIAESKIWDSEDTGLYDLTREGAEKINQKTELNPNIYYKTYTGVATHETQLGKHIADLGMEFTKILTGNYIGSVDDILWRPNDGLVSEISSQHPSDEKNISVDENSELHKGTWQVMPTMKGWDHSDFIGNDALDTKHSAIELTNFYHSISDYLMRIEKAES 637
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2hihB00 B:7-392  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee.......................hhhhhhhhh...eeee......hhhhhhhhhhhhhhheeee.hhhhhhhhh...eeeee............eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.....eeeeeee......hhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh......eeeee.ee.eee.....eee....hhhhhhhhhhhh...hhhhh......hhhhhh......eee...........eee...ee....hhhhh........hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------LIPASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hih B   7 AVQNPENPKNKDPFVFVHGFTGFVGEVAAKGENYWGGTKANLRNHLRKAGYETYEASVSALASNHERAVELYYYLKGGRVDYGAAHSEKYGHERYGKTYEGVLKDWKPGHPVHFIGHSMGGQTIRLLEHYLRFGDKAEIAYQQQHGGIISELFKGGQDNMVTSITTIATPHNGTHASDDIGNTPTIRNILYSFAQMSSHLGTIDFGMDHWGFKRKDGESLTDYNKRIAESKIWDSEDTGLYDLTREGAEKINQKTELNPNIYYKTYTGVATHETQLGKHIADLGMEFTKILTGNYIGSVDDILWRPNDGLVSEISSQHPSDEKNISVDENSELHKGTWQVMPTMKGWDHSDFIGNDALDTKHSAIELTNFYHSISDYLMRIEKAES 392
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386

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 '\|'

(no "SCOP Domain" information available for 2HIH)

Asymmetric 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)

Staphylococcus hyicus. Organism_taxid: 1284. (1)

1a	2hihB00	B:7-392
1b	2hihA00	A:7-393

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (LIP_STAHY | P04635)

molecular function
	GO:0052740	1-acyl-2-lysophosphatidylserine acylhydrolase activity	Catalysis of the reaction: 1-acyl-2-lysophosphatidylserine + H2O = sn-glycerol-phosphoserine + a carboxylate.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008970	phosphatidylcholine 1-acylhydrolase activity	Catalysis of the reaction: phosphatidylcholine + H2O = 2-acylglycerophosphocholine + a carboxylate.
	GO:0052739	phosphatidylserine 1-acylhydrolase activity	Catalysis of the reaction: phosphatidylserine + H2O = 2-acyl-sn-glycero-3-phosphoserine + fatty acid.
	GO:0004620	phospholipase activity	Catalysis of the hydrolysis of a glycerophospholipid.
	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.
	GO:0034638	phosphatidylcholine catabolic process	The chemical reactions and pathways resulting in the breakdown of phosphatidylcholines, any of a class of glycerophospholipids in which the phosphatidyl group is esterified to the hydroxyl group of choline.
	GO:0019433	triglyceride catabolic process	The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.
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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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

Biological Units
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	2hih
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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