2H5C - JenaLib

Title :   0.82A RESOLUTION CRYSTAL STRUCTURE OF ALPHA-LYTIC PROTEASE AT PH 5

Authors :   C. N. Fuhrmann, M. D. Daugherty, D. A. Agard

Date :   25 May 06 (Deposition) - 26 Sep 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.82

Chains :   Asym./Biol. Unit : A

Keywords :   A-Lytic Protease, Serine Protease, Acylation Transition State, Catalysis, Protein Folding, Protein Stability, Packing Distortion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. N. Fuhrmann, M. D. Daugherty, D. A. Agard
Subangstrom Crystallography Reveals That Short Ionic Hydrogen Bonds, And Not A His-Asp Low-Barrier Hydrogen Bond Stabilize The Transition State In Serine Protease Catalysis
J. Am. Chem. Soc. V. 128 9086 2006
PubMed-ID: 16834383 | Reference-DOI: 10.1021/JA057721O

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:48A , ARG A:120A , GLN A:237 , TYR A:238 , HOH A:389 , HOH A:390 , HOH A:391 , HOH A:485 , HOH A:534 , HOH A:559 , HOH A:568 , HOH A:596 , HOH A:635 , HOH A:698 , HOH A:707 , HOH A:718 , HOH A:719	BINDING SITE FOR RESIDUE SO4 A 246
02	AC2	SOFTWARE	ALA A:15A , ASN A:15B , ARG A:230 , PRO A:233 , HOH A:333 , HOH A:403 , HOH A:434 , HOH A:460 , HOH A:488 , HOH A:509 , HOH A:633 , HOH A:634 , HOH A:643	BINDING SITE FOR RESIDUE SO4 A 247
03	AC3	SOFTWARE	HIS A:57 , ARG A:122 , ARG A:192 , GLY A:193 , SER A:195 , GOL A:253 , HOH A:424 , HOH A:459 , HOH A:491 , HOH A:668 , HOH A:669 , HOH A:670 , HOH A:671 , HOH A:676	BINDING SITE FOR RESIDUE SO4 A 248
04	AC4	SOFTWARE	THR A:59A , VAL A:59B , ARG A:90 , HOH A:386 , HOH A:393 , HOH A:468 , HOH A:562 , HOH A:626 , HOH A:627 , HOH A:708	BINDING SITE FOR RESIDUE SO4 A 203
05	AC5	SOFTWARE	ALA A:48C , THR A:49 , SER A:110 , ALA A:176 , ARG A:178 , HOH A:309 , HOH A:349 , HOH A:461 , HOH A:555 , HOH A:573 , HOH A:661 , HOH A:662 , HOH A:730	BINDING SITE FOR RESIDUE SO4 A 204
06	AC6	SOFTWARE	THR A:168 , ARG A:178 , HOH A:417 , HOH A:549 , HOH A:709 , HOH A:731	BINDING SITE FOR RESIDUE SO4 A 205
07	AC7	SOFTWARE	GLN A:219 , SER A:219A , HOH A:353 , HOH A:355 , HOH A:630 , HOH A:700	BINDING SITE FOR RESIDUE SO4 A 206
08	AC8	SOFTWARE	ASN A:36 , THR A:62 , ARG A:65 , HOH A:365 , HOH A:599 , HOH A:701 , HOH A:702	BINDING SITE FOR RESIDUE SO4 A 249
09	AC9	SOFTWARE	ALA A:131 , VAL A:132 , LYS A:165 , HOH A:566 , HOH A:646 , HOH A:703 , HOH A:711	BINDING SITE FOR RESIDUE SO4 A 250
10	BC1	SOFTWARE	ARG A:141 , HOH A:314 , HOH A:380 , HOH A:432 , HOH A:527 , HOH A:528 , HOH A:529 , HOH A:548 , HOH A:567 , HOH A:590 , HOH A:611 , HOH A:623 , HOH A:665 , HOH A:674 , HOH A:712	BINDING SITE FOR RESIDUE SO4 A 251
11	BC2	SOFTWARE	ASN A:217 , GLN A:219 , HOH A:569 , HOH A:679 , HOH A:720 , HOH A:721 , HOH A:722	BINDING SITE FOR RESIDUE SO4 A 252
12	BC3	SOFTWARE	HIS A:57 , ARG A:122 , TYR A:171 , GLU A:174 , ARG A:192 , SER A:214 , GLY A:215 , SO4 A:248 , HOH A:337 , HOH A:474 , HOH A:477 , HOH A:491 , HOH A:629 , HOH A:671 , HOH A:745	BINDING SITE FOR RESIDUE GOL A 253
13	BC4	SOFTWARE	PHE A:120I , VAL A:120J , THR A:120K , ALA A:173 , GLU A:174 , HOH A:489 , HOH A:531 , HOH A:532 , HOH A:576	BINDING SITE FOR RESIDUE GOL A 254

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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 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 d2h5ca_ A: alpha-Lytic protease                                                                                                                                                                        SCOP domains
               CATH domains --2h5cA01 A:16-119,A:231-243 Trypsin-like serine proteases                  2h5cA02 A:120-230 Trypsin-like serine proteases                                                            2h5cA01      -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee...eeee..eeeee..eeeeeehhhhh....eeee..eeeeeeeeee.....eeeeee....eeeeeeee..eeee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eee.....eeeeeeee...........hhhhh.eeeeehhhhhhhhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------TRYPSI---------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2h5c A  15A ANIVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSAQTLLPRVANGSSFVTVRGSTEAAVGAAVCRSGRTTGYQCGTITAKNVTANYAEGAVRGLTQGNACMGRGDSGGSWITSAGQAQGVMSGGNVQSNGNNCGIPASQRSSLFERLQPILSQYGLSLVTG  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

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	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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

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