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Description

Title :   CRYSTAL STRUCTURE OF THE SECOND TETRAHEDRAL INTERMEDIATES OF SGPB AT PH 4.2

Authors :   T. W. Lee, M. N. G. James

Date :   14 Jun 07 (Deposition) - 11 Dec 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.18

Chains :   Asym. Unit : E,I
Biol. Unit 1: E,I  (2x)
Biol. Unit 2: E,I  (1x)

Keywords :   Chymotrypsin-Type Serine Peptidase, Second Tetrahedral Intermediate, Tetrapeptide, Beta Barrels, Alpha Helix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. W. Lee, M. N. James
1. 2A-Resolution Crystal Structures Reveal The Second Tetrahedral Intermediates Of Streptogrisin B (Sgpb).
Biochim. Biophys. Acta V. 1784 319 2008
PubMed-ID: 18157955 | Reference-DOI: 10.1016/J.BBAPAP.2007.11.012

Compounds

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

Molecule 2 - 4-MER PEPTIDE DAIY
	Chains	:	I
	Organism Scientific	:	STREPTOMYCES GRISEUS
	Organism Taxid	:	1911
	Other Details	:	AUTO-PROTEOLYTIC PRODUCT

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	E	I
Biological Unit 1 (2x)	:	E	I
Biological Unit 2 (1x)	:	E	I

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 9)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	2	Ligand/Ion	GLYCEROL
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	SO4	2	Ligand/Ion	SULFATE ION

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR E:163 , ARG E:182 , HOH E:459 , HOH E:659	BINDING SITE FOR RESIDUE CL E 411
2	AC2	SOFTWARE	ARG E:81	BINDING SITE FOR RESIDUE CL E 412
3	AC3	SOFTWARE	ARG E:139 , GLY E:156 , THR E:157 , GOL E:401 , HOH E:655	BINDING SITE FOR RESIDUE SO4 E 421
4	AC4	SOFTWARE	ARG E:208 , HOH E:463 , HOH E:489 , HOH E:564 , HOH E:592 , HOH E:651	BINDING SITE FOR RESIDUE SO4 E 422
5	AC5	SOFTWARE	SER E:33 , THR E:39 , GLY E:40 , CYS E:42 , HOH E:514	BINDING SITE FOR RESIDUE EDO E 431
6	AC6	SOFTWARE	GLY E:40 , ARG E:41 , PRO E:192B , SER E:221	BINDING SITE FOR RESIDUE EDO E 432
7	AC7	SOFTWARE	HIS E:57 , ASP E:60 , HOH E:519 , HOH E:630 , HOH E:674 , ILE I:3	BINDING SITE FOR RESIDUE EDO E 433
8	AC8	SOFTWARE	THR E:64 , THR E:65 , TRP E:67 , VAL E:132 , HOH E:477 , HOH E:531 , HOH E:534 , HOH E:641	BINDING SITE FOR RESIDUE EDO E 434
9	AC9	SOFTWARE	GLY E:19 , ASP E:29 , ARG E:139 , GLY E:140 , SER E:141 , THR E:143 , GLY E:156 , THR E:157 , HIS E:158 , SO4 E:421 , HOH E:453 , HOH E:541 , HOH E:549 , HOH E:621	BINDING SITE FOR RESIDUE GOL E 401

SS Bonds (2, 2)

Asymmetric Unit

No.	Residues
1	E:42	-	E:58
2	E:191	-	E:220

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Phe E:94	-	Pro E:99A

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2QA9)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRTB_STRGR	143-148	1	E:53-58
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRTB_STRGR	249-260	1	E:191-200

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRTB_STRGR	143-148	2	E:53-58
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRTB_STRGR	249-260	2	E:191-200

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRTB_STRGR	143-148	1	E:53-58
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRTB_STRGR	249-260	1	E:191-200

Exons (0, 0)

(no "Exon" information available for 2QA9)

Sequences/Alignments

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 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 d2qa9e_ E: automated matches                                                                                                                                                              SCOP domains
               CATH domains 2qa9E01 E:16-116,E:231-242 Trypsin-like serine proteases                     2qa9E02 E:117-230 Trypsin-like serine proteases                                                2qa9E01       CATH domains
               Pfam domains Trypsin-2qa9E01 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 ----------------------------TRYPSI----------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qa9 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:4
                                     
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                2qa9 I    1 DAIY    4

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: Prokaryotic proteases (131)

Protein domain: automated matches (19)

Streptomyces griseus [TaxId: 1911] (8)

d2qa9e_

CATH Domains (1, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

1a	2qa9E02	E:117-230
1b	2qa9E01	E:16-116,E:231-242

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_PA (797)

Family: Trypsin (679)

Streptomyces griseus (24)

Trypsin-2qa9E01

E:16-236

Gene Ontology (6, 6)

Asymmetric 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.

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	2qa9
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	PRTB_STRGR \| P00777	:	1cso 1ct0 1ct2 1ct4 1ds2 1sgd 1sge 1sgn 1sgp 1sgq 1sgr 1sgy 2gkv 2nu0 2nu1 2nu2 2nu3 2nu4 2qaa 2sgd 2sge 2sgf 2sgp 2sgq 3sgb 3sgq 4sgb

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QA9)