3URE - JenaLib

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Title :   REPACK MUTANT (T181I, W199L, Q210I) OF ALPHA-LYTIC PROTEASE

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

Date :   22 Nov 11 (Deposition) - 23 May 12 (Release) - 18 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.49

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

Keywords :   Serine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Kelch, N. L. Salimi, D. A. Agard
Functional Modulation Of A Protein Folding Landscape Via Side-Chain Distortion.
Proc. Natl. Acad. Sci. Usa V. 109 9414 2012
PubMed-ID: 22635267 | Reference-DOI: 10.1073/PNAS.1119274109

Molecule 1 - ALPHA-LYTIC PROTEASE
	Chains	:	A, B
	EC Number	:	3.4.21.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ALPHA-LP
	Mutation	:	YES
	Organism Scientific	:	LYSOBACTER ENZYMOGENES
	Organism Taxid	:	69
	Synonym	:	ALPHA-LYTIC ENDOPEPTIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:217 , GLN A:219 , HOH A:483 , HOH A:523 , HOH A:652 , HOH A:693 , HOH A:712	BINDING SITE FOR RESIDUE SO4 A 301
2	AC2	SOFTWARE	ASN A:36 , THR A:62 , ARG A:65 , HOH A:452	BINDING SITE FOR RESIDUE SO4 A 302
3	AC3	SOFTWARE	ARG A:178 , HOH A:403 , HOH A:567 , HOH A:726 , THR B:168 , ARG B:178 , HOH B:726	BINDING SITE FOR RESIDUE SO4 A 303
4	AC4	SOFTWARE	HIS A:57 , ARG A:192 , GLY A:193 , SER A:195 , HOH A:418 , HOH A:453 , HOH A:695	BINDING SITE FOR RESIDUE SO4 A 304
5	AC5	SOFTWARE	ALA A:39 , ARG A:192 , GLY B:120E , SER B:120G , ARG B:122 , HOH B:607 , HOH B:608 , HOH B:610 , HOH B:614 , HOH B:646 , HOH B:874	BINDING SITE FOR RESIDUE SO4 B 501
6	AC6	SOFTWARE	ARG B:120A , HOH B:829	BINDING SITE FOR RESIDUE SO4 B 502
7	AC7	SOFTWARE	HIS B:57 , ARG B:192 , GLY B:193 , SER B:195 , HOH B:758 , HOH B:818 , HOH B:855	BINDING SITE FOR RESIDUE SO4 B 503

Asymmetric Unit

No.	Residues
1	A:42	-	A:58
2	A:137	-	A:159
3	A:189	-	A:220A
4	B:42	-	B:58
5	B:137	-	B:159
6	B:189	-	B:220A

Asymmetric Unit

No.	Residues
1	Phe A:94	-	Pro A:95
2	Phe B:94	-	Pro B:95

(no "SAP(SNP)/Variant" information available for 3URE)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRLA_LYSEN	231-236	2	A:53-58 B:53-58
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRLA_LYSEN	336-347	2	A:189-200 B:189-200

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	PRLA_LYSEN	231-236	1	A:53-58 -
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRLA_LYSEN	336-347	1	A:189-200 -

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.	PRLA_LYSEN	231-236	1	- B:53-58
2	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	PRLA_LYSEN	336-347	1	- B:189-200

(no "Exon" information available for 3URE)

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:198
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:198
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
          PRLA_LYSEN    200 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG  397
               SCOP domains d3urea_ A: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee...eeee..eeeee..eeeeeehhhhh....eeee..eeeeeeeeee.....eeeeee....eeeeeeee..eeee..ee.......eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eee....eeeeeeeee...........hhhhh.eeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3ure A  15A ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLIQGNACMGRGDSGGSLITSAGQAIGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG  245
                            ||   || 34 ||    44A    ||| 51       59B  ||  ||83 || |  |95|      109    ||120C|||||||123 ||    136      |158       168  ||   179     ||192      201A||     215    ||220A  |||  227       237        
                            ||  19|   36|    44A  48A||         59A| 62| 67|  85| | 91|||           114| ||||120I||  125|           143|            171|         185|         201A||         219A||| |  |||                       
                          15A|   31    38          48B|          59B  64  81   87 |  94||            119 |||||120J|   129            156             173          189           202|          219B|| |  |||                       
                           15B                      48C                         88A   95|             120A|||||120K                                                              207           219C| |  |||                       
                                                                                      100              120B|||||                                                                                219D |  |||                       
                                                                                                        120C||||                                                                                  220A  |||                       
                                                                                                         120D|||                                                                                     222A||                       
                                                                                                          120E||                                                                                      222B|                       
                                                                                                           120G|                                                                                       222C                       
                                                                                                            120H

Chain B from PDB  Type:PROTEIN  Length:198
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:198
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
          PRLA_LYSEN    200 ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG  397
               SCOP domains d3ureb_ B: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee...eeee..eeeee..eeeeeehhhhh....eeee..eeeeeeeeee.....eeeeee....eeeeeeee..eeee..ee.......eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eee....eeeeeeeee...........hhhhh.eeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3ure B  15A ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLIQGNACMGRGDSGGSLITSAGQAIGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG  245
                            ||   || 34 ||    44A    ||| 51       59B  ||  ||83 || |  |95|      109    ||120C|||||||123 ||    136      |158       168  ||   179     ||192      201A||     215    ||220A  |||  227       237        
                          15A|  19|   36|    44A  48A||         59A| 62| 67|  85| | 91|||           114| ||||120I||  125|           143|            171|         185|         201A||         219A||| |  |||                       
                           15B   31    38          48B|          59B  64  81   87 |  94||            119 |||||120J|   129            156             173          189           202|          219B|| |  |||                       
                                                    48C                         88A   95|             120A|||||120K                                                              207           219C| |  |||                       
                                                                                      100              120B|||||                                                                                219D |  |||                       
                                                                                                        120C||||                                                                                  220A  |||                       
                                                                                                         120D|||                                                                                     222A||                       
                                                                                                          120E||                                                                                      222B|                       
                                                                                                           120G|                                                                                       222C                       
                                                                                                            120H

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: Prokaryotic proteases (131)

Protein domain: alpha-Lytic protease (45)

Lysobacter enzymogenes, 495 [TaxId: 69] (45)

1a	d3urea_	A:
1b	d3ureb_	B:

(no "CATH Domain" information available for 3URE)

(no "Pfam Domain" information available for 3URE)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRLA_LYSEN | P00778)

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.

Asymmetric Unit
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	3.4.21.12
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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