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Title :   MOLECULAR STRUCTURES OF THE COMPLEXES OF SGPB WITH OMTKY3 AROMATIC P1 VARIANTS TRP18I, HIS18I, PHE18I AND TYR18I

Authors :   K. S. Bateman, S. Anderson, W. Lu, M. A. Qasim, K. Huang, M. Laskowski Jr. , M. N. G. James

Date :   08 Nov 06 (Deposition) - 21 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : E,I

Keywords :   Enzyme-Inhibitor Complex, Aromatic P1 Residue, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Bateman, S. Anderson, W. Lu, M. A. Qasim, K. Huang, M. Laskowski Jr. , M. N. G. James
Molecular Structures Of The Complexes Of Sgpb With Omtky3 Aromatic P1 Variants Trp18I, His18I, Phe18I And Tyr18I
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - STREPTOGRISIN B
	Chains	:	E
	EC Number	:	3.4.21.81
	Fragment	:	RESIDUES 115-299
	Organism Scientific	:	STREPTOMYCES GRISEUS
	Organism Taxid	:	1911
	Synonym	:	PROTEASE B, SGPB, PRONASE ENZYME B

Molecule 2 - OVOMUCOID
	Chains	:	I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEZZ318.TKY
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	THIRD DOMAIN, RESIDUES 135-185
	Mutation	:	YES
	Organism Common	:	TURKEY
	Organism Scientific	:	MELEAGRIS GALLOPAVO
	Organism Taxid	:	9103
	Synonym	:	FRAGMENT

		1	2
Asymmetric/Biological Unit	:	E	I

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NU1)

(no "Site" information available for 2NU1)

Asymmetric/Biological Unit

No.	Residues
1	E:42	-	E:58
2	E:191	-	E:220
3	I:8	-	I:38
4	I:16	-	I:35
5	I:24	-	I:56

Asymmetric/Biological Unit

No.	Residues
1	Phe E:94	-	Pro E:99A
2	Tyr I:11	-	Pro I:12

(no "SAP(SNP)/Variant" information available for 2NU1)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KAZAL_1	PS00282	Kazal serine protease inhibitors family signature.	IOVO_MELOE	16-38	1	I:16-38
1	KAZAL_1	PS00282	Kazal serine protease inhibitors family signature.	IOVO_MELGA	86-108 145-167	1	- I:16-38
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRTB_STRGR	143-148	1	E:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRTB_STRGR	249-260	1	E:191-200

(no "Exon" information available for 2NU1)

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 E from PDB  Type:PROTEIN  Length:185
 aligned with PRTB_STRGR | P00777 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:185
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294     
          PRTB_STRGR    115 ISGGDAIYSSTGRCSLGFNVRSGSTYYFLTAGHCTDGATTWWANSARTTVLGTTSGSSFPNNDYGIVRYTNTTIPKDGTVGGQDITSAANATVGMAVTRRGSTTGTHSGSVTALNATVNYGGGDVVYGMIRTNVCAEPGDSGGPLYSGTRAIGLTSGGSGNCSSGGTTFFQPVTEALSAYGVSVY  299
               SCOP domains d2nu1e_ E: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2nu1E01 E:16-116,E:231-242 Trypsin-like serine proteases                     2nu1E02 E:117-230 Trypsin-like serine proteases                                                2nu1E01       CATH domains
               Pfam domains Trypsin-2nu1E01 E:16-236                                                                                                                                                           ------ Pfam domains
         Sec.struct. author .....eee....eee..eeeee..eeeeeehhhhhh...eee.......eeeeeeeee.....eeeeee.........ee..ee..ee.......eeeeee...eeeeeeeeeeeeeee.....eeeeeeee...........eeee..eeeeeeeeeeee...eeeeeeeehhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------TRYPSI------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2nu1 E   16 ISGGDAIYSSTGRCSLGFNVRSGSTYYFLTAGHCTDGATTWWANSARTTVLGTTSGSSFPNNDYGIVRYTNTTIPKDGTVGGQDITSAANATVGMAVTRRGSTTGTHSGSVTALNATVNYGGGDVVYGMIRTNVCAEPGDSGGPLYSGTRAIGLTSGGSGNCSSGGTTFFQPVTEALSAYGVSVY  242
                               ||   34|       48||||    54     || 65  ||    84      |99A       109       119       129       139   ||  161       171       181  ||  |194       208       218       228       237     
                              19|   34|       48A|||          60|    68|           91|||                                         143|                         184|  ||       202|                         235A       
                               29    39        48B||           62     78            93||                                          156                          190  ||        207                                    
                                                48C|                                 94|                                                                         192A|                                               
                                                 48D                                 99A                                                                          192B

Chain I from PDB  Type:PROTEIN  Length:51
 aligned with IOVO_MELGA | P68390 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:51
                                   144       154       164       174       184 
          IOVO_MELGA    135 VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC  185
               SCOP domains d2nu1i1 I:6-56 Ovomucoid domains                    SCOP domains
               CATH domains 2nu1I00 I:6-56  [code=3.30.60.30, no name defined]  CATH domains
               Pfam domains --Kazal_1-2nu1I01 I:8-56                            Pfam domains
         Sec.struct. author ..........ee.....eee....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------KAZAL_1  PDB: I:16-38  ------------------ PROSITE
                 Transcript --------------------------------------------------- Transcript
                2nu1 I    6 VDCSEYPKPACTHEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC   56
                                    15        25        35        45        55

Chain I from PDB  Type:PROTEIN  Length:51
 aligned with IOVO_MELOE | P68436 from UniProtKB/Swiss-Prot  Length:56

    Alignment length:51
                                    15        25        35        45        55 
          IOVO_MELOE      6 VDCSEYPKPACTLEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC   56
               SCOP domains d2nu1i1 I:6-56 Ovomucoid domains                    SCOP domains
               CATH domains 2nu1I00 I:6-56  [code=3.30.60.30, no name defined]  CATH domains
               Pfam domains --Kazal_1-2nu1I01 I:8-56                            Pfam domains
         Sec.struct. author ..........ee.....eee....ee.hhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------KAZAL_1  PDB: I:16-38  ------------------ PROSITE
                 Transcript --------------------------------------------------- Transcript
                2nu1 I    6 VDCSEYPKPACTHEYRPLCGSDNKTYGNKCNFCNAVVESNGTLTLSHFGKC   56
                                    15        25        35        45        55

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Wheat Germ Agglutinin (Isolectin 2); domain 1 (140)

Homologous Superfamily: [code=3.30.60.30, no name defined] (93)

Streptomyces griseus. Organism_taxid: 1911. (4)

2nu1I00

I:6-56

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Trypsin-like serine proteases (1488)

Streptomyces griseus. Organism_taxid: 1911. (5)

2a	2nu1E02	E:117-230
2b	2nu1E01	E:16-116,E:231-242

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Kazal (46)

Family: Kazal_1 (34)

Meleagris ocellata (Ocellated turkey) (Agriocharis ocellata) (2)

Kazal_1-2nu1I01

I:8-56

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Streptomyces griseus (24)

Trypsin-2nu1E01

E:16-236

Asymmetric/Biological Unit(hide GO term definitions)

Chain E (PRTB_STRGR | P00777)

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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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 I (IOVO_MELOE | P68436)

molecular function
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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 I (IOVO_MELGA | P68390)

molecular function
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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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	Cis Peptide Bonds
		Phe E:94 - Pro E:99A	[ RasMol ]
		Tyr I:11 - Pro I:12	[ RasMol ]

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1sgy	TYR 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B AT PH 6.5
2nu0	MOLECULAR STRUCTURES OF THE COMPLEXES OF SGPB WITH OMTKY3 AROMATIC P1 VARIANTS TRP18I, HIS18I, PHE18I, AND TYR18I
2nu2	ACCOMMODATION OF POSITIVELY-CHARGED RESIDUES IN A HYDROPHOBIC SPECIFICITY POCKET: CRYSTAL STRUCTURES OF SGPB IN COMPLEX WITH OMTKY3 VARIANTS LYS18I AND ARG18I
2nu3	ACCOMMODATION OF POSITIVELY-CHARGED RESIDUES IN A HYDROPHOBIC SPECIFICITY POCKET: CRYSTAL STRUCTURES OF SGPB IN COMPLEX WITH OMTKY3 VARIANTS LYS18I AND ARG18I
2nu4	ACCOMMODATION OF POSITIVELY-CHARGED RESIDUES IN A HYDROPHOBIC SPECIFICITY POCKET: CRYSTAL STRUCTURES OF SGPB IN COMPLEX WITH OMTKY3 VARIANTS LYS18I AND ARG18I
2sgf	PHE 18 VARIANT OF TURKEY OVOMUCOID INHIBITOR THIRD DOMAIN COMPLEXED WITH STREPTOMYCES GRISEUS PROTEINASE B
3sgb	STRUCTURE OF THE COMPLEX OF STREPTOMYCES GRISEUS PROTEASE B AND THE THIRD DOMAIN OF THE TURKEY OVOMUCOID INHIBITOR AT 1.8 ANGSTROMS RESOLUTION

Description

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (2, 3)

Pfam Domains (2, 2)

Gene Ontology (10, 16)

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