2PFE - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THERMOBIFIDA FUSCA PROTEASE A (TFPA)

Authors :   B. A. Kelch, D. A. Agard

Date :   04 Apr 07 (Deposition) - 03 Jul 07 (Release) - 06 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.44

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

Keywords :   Beta-Barrels; Serine Protease; Thermophile; Kinetic Stability; Thermostability; Protein Folding; Alpha-Lytic Protease; Folding Transition State Structure, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Kelch, D. A. Agard
Mesophile Versus Thermophile: Insights Into The Structural Mechanisms Of Kinetic Stability
J. Mol. Biol. V. 370 784 2007
PubMed-ID: 17543987 | Reference-DOI: 10.1016/J.JMB.2007.04.078

Molecule 1 - ALKALINE SERINE PROTEASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	STREPTOMYCES LIVIDANS
	Expression System Plasmid	:	PGL-1
	Expression System Taxid	:	1916
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 183-368
	Gene	:	TFPA
	Organism Scientific	:	THERMOBIFIDA FUSCA
	Organism Taxid	:	269800
	Other Details	:	SECRETED WITH N-TERMINAL, COVALENTLY ATTACHED PRO REGION NECESSARY FOR FOLDING AND SECRETION
	Strain	:	YX
	Synonym	:	PROTEASE A; TFPA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	AES	2	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	AES	1	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	AES	1	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	AES	1	Ligand/Ion	4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:131 , THR A:132 , LYS A:165 , ALA B:131 , THR B:132 , LYS B:165 , SO4 B:401 , HOH B:1216	BINDING SITE FOR RESIDUE SO4 A 400
2	AC2	SOFTWARE	ALA A:131 , THR A:132 , LYS A:165 , SO4 A:400 , ALA B:131 , THR B:132 , LYS B:165	BINDING SITE FOR RESIDUE SO4 B 401
3	AC3	SOFTWARE	HIS B:57 , ASP B:194 , SER B:195 , THR B:213 , SER B:214 , GLY B:215 , GLY B:216 , GLY B:218 , HOH B:1292	BINDING SITE FOR RESIDUE AES B 1001
4	AC4	SOFTWARE	HIS A:57 , ALA A:190 , ASP A:194 , SER A:195 , THR A:213 , SER A:214 , GLY A:215 , GLY A:218 , HOH A:1154 , HOH A:1202	BINDING SITE FOR RESIDUE AES A 1002
5	AC5	SOFTWARE	SER A:164 , GLN A:167 , ARG A:182 , HOH A:1206 , PHE B:94 , HOH B:1076 , HOH B:1132 , HOH B:1186 , HOH B:1208	BINDING SITE FOR RESIDUE GOL B 402
6	AC6	SOFTWARE	GLN A:167 , THR A:168 , VAL A:169 , ARG A:182 , HOH A:1320 , HOH A:1344 , TYR B:91 , TYR B:237 , HOH B:1048	BINDING SITE FOR RESIDUE GOL A 403

Asymmetric Unit

No.	Residues
1	A:42	-	A:58
2	A:137	-	A:159
3	A:189	-	A:219A
4	B:42	-	B:58
5	B:137	-	B:159
6	B:189	-	B:219A

Asymmetric Unit

No.	Residues
1	Ser A:66	-	Pro A:67
2	Phe A:94	-	Pro A:95
3	Ser B:66	-	Pro B:67
4	Phe B:94	-	Pro B:95

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

(no "PROSITE Motif" information available for 2PFE)

(no "Exon" information available for 2PFE)

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:186
 aligned with O86984_THEFU | O86984 from UniProtKB/TrEMBL  Length:368

    Alignment length:186
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
        O86984_THEFU    183 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  368
               SCOP domains d2pfea_ A: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2pfeA01 A:15-119,A:231-245 Trypsin-like serine proteases                2pfeA02 A:120-230 Trypsin-like serine proteases                                                    2pfeA01         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee..eeee..eeeee..eeeeeehhhhh....ee....eeeeeee.....eeeeee....eeeeeee.....eee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeeeeee...eeeeeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2pfe A   15 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  245
                             |   || 34 ||     45   |||  52       |60 ||   ||88|  ||||103       113|| |||120G||||   129       139   ||  161       171|      182  ||   195      |209       219|||    229       239      
                             |  19|   36|   44A  48A||         59A| 62|  68|| | 91|||           114| ||||120H|||  125|           143|            171|         185|         201A|         219A||                       
                           15B   31    39         48B|          59B  64   85| |  94||            119 |||||120I||   129            156             173          189           207           220|                       
                                                   48C                     87 |   95|             120A|||||120J|                                                                            222                       
                                                                            88A   100              120B|||||120K                                                                                                      
                                                                                                    120C||||                                                                                                          
                                                                                                     120D|||                                                                                                          
                                                                                                      120E||                                                                                                          
                                                                                                       120F|                                                                                                          
                                                                                                        120G

Chain A from PDB  Type:PROTEIN  Length:186
 aligned with Q47SP5_THEFY | Q47SP5 from UniProtKB/TrEMBL  Length:368

    Alignment length:186
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
        Q47SP5_THEFY    183 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  368
               SCOP domains d2pfea_ A: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2pfeA01 A:15-119,A:231-245 Trypsin-like serine proteases                2pfeA02 A:120-230 Trypsin-like serine proteases                                                    2pfeA01         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee..eeee..eeeee..eeeeeehhhhh....ee....eeeeeee.....eeeeee....eeeeeee.....eee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeeeeee...eeeeeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2pfe A   15 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  245
                             |   || 34 ||     45   |||  52       |60 ||   ||88|  ||||103       113|| |||120G||||   129       139   ||  161       171|      182  ||   195      |209       219|||    229       239      
                           15B  19|   36|   44A  48A||         59A| 62|  68|| | 91|||           114| ||||120H|||  125|           143|            171|         185|         201A|         219A||                       
                                 31    39         48B|          59B  64   85| |  94||            119 |||||120I||   129            156             173          189           207           220|                       
                                                   48C                     87 |   95|             120A|||||120J|                                                                            222                       
                                                                            88A   100              120B|||||120K                                                                                                      
                                                                                                    120C||||                                                                                                          
                                                                                                     120D|||                                                                                                          
                                                                                                      120E||                                                                                                          
                                                                                                       120F|                                                                                                          
                                                                                                        120G

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with O86984_THEFU | O86984 from UniProtKB/TrEMBL  Length:368

    Alignment length:186
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
        O86984_THEFU    183 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  368
               SCOP domains d2pfeb_ B: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2pfeB01 B:15-119,B:231-245 Trypsin-like serine proteases                2pfeB02 B:120-230 Trypsin-like serine proteases                                                    2pfeB01         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee..eeee..eeeee..eeeeeehhhhh....ee....eeeeeee.....eeeeee....eeeeeee.....eee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeeeeee...eeeeeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2pfe B   15 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  245
                             |   || 34 ||     45   |||  52       |60 ||   ||88|  ||||103       113|| |||120G||||   129       139   ||  161       171|      182  ||   195      |209       219|||    229       239      
                           15B  19|   36|   44A  48A||         59A| 62|  68|| | 91|||           114| ||||120H|||  125|           143|            171|         185|         201A|         219A||                       
                                 31    39         48B|          59B  64   85| |  94||            119 |||||120I||   129            156             173          189           207           220|                       
                                                   48C                     87 |   95|             120A|||||120J|                                                                            222                       
                                                                            88A   100              120B|||||120K                                                                                                      
                                                                                                    120C||||                                                                                                          
                                                                                                     120D|||                                                                                                          
                                                                                                      120E||                                                                                                          
                                                                                                       120F|                                                                                                          
                                                                                                        120G

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with Q47SP5_THEFY | Q47SP5 from UniProtKB/TrEMBL  Length:368

    Alignment length:186
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362      
        Q47SP5_THEFY    183 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  368
               SCOP domains d2pfeb_ B: automated matches                                                                                                                                                               SCOP domains
               CATH domains 2pfeB01 B:15-119,B:231-245 Trypsin-like serine proteases                2pfeB02 B:120-230 Trypsin-like serine proteases                                                    2pfeB01         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee..eeee..eeeee..eeeeeehhhhh....ee....eeeeeee.....eeeeee....eeeeeee.....eee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeeeeee...eeeeeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2pfe B   15 AAIIGGNPYYFGNYRCSIGFSVRQGSQTGFATAGHCGSTGTRVSSPSGTVAGSYFPGRDMGWVRITSADTVTPLVNRYNGGTVTVTGSQEAATGSSVCRSGATTGWRCGTIQSKNQTVRYAEGTVTGLTRTTACAEGGDSGGPWLTGSQAQGVTSGGTGDCRSGGITFFQPINPLLSYFGLQLVTG  245
                             |   || 34 ||     45   |||  52       |60 ||   ||88|  ||||103       113|| |||120G||||   129       139   ||  161       171|      182  ||   195      |209       219|||    229       239      
                           15B  19|   36|   44A  48A||         59A| 62|  68|| | 91|||           114| ||||120H|||  125|           143|            171|         185|         201A|         219A||                       
                                 31    39         48B|          59B  64   85| |  94||            119 |||||120I||   129            156             173          189           207           220|                       
                                                   48C                     87 |   95|             120A|||||120J|                                                                            222                       
                                                                            88A   100              120B|||||120K                                                                                                      
                                                                                                    120C||||                                                                                                          
                                                                                                     120D|||                                                                                                          
                                                                                                      120E||                                                                                                          
                                                                                                       120F|                                                                                                          
                                                                                                        120G

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Trypsin-like serine proteases (1752)

Superfamily: Trypsin-like serine proteases (1752)

Family: automated matches (71)

Protein domain: automated matches (71)

Thermobifida fusca YX [TaxId: 269800] (1)

1a	d2pfea_	A:
1b	d2pfeb_	B:

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)

Thermobifida fusca yx. Organism_taxid: 269800. Strain: yx. (1)

1a	2pfeA02	A:120-230
1b	2pfeB02	B:120-230
1c	2pfeA01	A:15-119,A:231-245
1d	2pfeB01	B:15-119,B:231-245

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (O86984_THEFU | O86984)

molecular function
	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 A,B (Q47SP5_THEFY | Q47SP5)

molecular function
	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.

Asymmetric Unit
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	Cis Peptide Bonds
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		Phe B:94 - Pro B:95	[ RasMol ]
		Ser A:66 - Pro A:67	[ RasMol ]
		Ser B:66 - Pro B:67	[ RasMol ]

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Access by PDB/NDB ID
	2pfe
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(no "Entries Sharing at Least One Protein Chain" available for 2PFE)

1ssx	MESOPHILIC, KINETICALLY STABLE HOMOLOG (ALPHA-LYTIC PROTEASE)
2oua	ACID RESISTANT, KINETICALLY STABLE HOMOLOG (NAPASE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (6, 6)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 4)

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Gene Ontology (5, 9)

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Related Entries Specified in the PDB File