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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURAL ANALYSIS OF SERRATIA PROTEASE

Authors :   K. Hamada, H. Hiramatsu, Y. Katsuya, Y. Hata, Y. Katsube

Date :   02 Nov 94 (Deposition) - 14 Feb 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

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

Reference :   K. Hamada, Y. Hata, Y. Katsuya, H. Hiramatsu, T. Fujiwara, Y. Katsube
Crystal Structure Of Serratia Protease, A Zinc-Dependent Proteinase From Serratia Sp. E-15, Containing A Beta-Sheet Coil Motif At 2. 0 A Resolution.
J. Biochem. (Tokyo) V. 119 844 1996
PubMed-ID: 8797082
(for further references see the PDB file header)

Molecule 1 - SERRALYSIN
	Chains	:	A
	EC Number	:	3.4.24.40
	Engineered	:	YES
	Organism Scientific	:	SERRATIA SP.
	Organism Taxid	:	617
	Strain	:	E-15

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CA	7	Ligand/Ion	CALCIUM ION
2	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:253 , GLY A:255 , THR A:257 , ASP A:285 , GLY A:287 , ASP A:290	BINDING SITE FOR RESIDUE CA A 911
2	AC2	SOFTWARE	GLY A:288 , ASP A:290 , THR A:327 , GLU A:329 , HOH A:524 , HOH A:550	BINDING SITE FOR RESIDUE CA A 912
3	AC3	SOFTWARE	GLY A:334 , GLY A:336 , ASP A:338 , GLY A:351 , ALA A:353 , ASP A:356	BINDING SITE FOR RESIDUE CA A 913
4	AC4	SOFTWARE	ASN A:343 , ALA A:345 , ASN A:347 , GLY A:360 , GLY A:362 , ASP A:365	BINDING SITE FOR RESIDUE CA A 914
5	AC5	SOFTWARE	GLY A:352 , GLY A:354 , ASP A:356 , GLY A:369 , ALA A:371 , ASP A:374	BINDING SITE FOR RESIDUE CA A 915
6	AC6	SOFTWARE	GLY A:361 , GLY A:362 , GLY A:363 , ASP A:365 , ASP A:383 , ASP A:390 , HOH A:604	BINDING SITE FOR RESIDUE CA A 916
7	AC7	SOFTWARE	GLY A:370 , GLY A:372 , ASP A:374 , ASP A:400	BINDING SITE FOR RESIDUE CA A 917
8	AC8	SOFTWARE	HIS A:176 , HIS A:180 , HIS A:186 , TYR A:216 , HOH A:557	BINDING SITE FOR RESIDUE ZN A 920
9	CAT	UNKNOWN	HIS A:176 , HIS A:180 , HIS A:186 , TYR A:216	NULL

(no "SS Bond" information available for 1SRP)

(no "Cis Peptide Bond" information available for 1SRP)

(no "SAP(SNP)/Variant" information available for 1SRP)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	PRZN_SERME	189-198	1	A:173-182
2	HEMOLYSIN_CALCIUM	PS00330	Hemolysin-type calcium-binding region signature.	PRZN_SERME	372-390	1	A:356-374

(no "Exon" information available for 1SRP)

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:468
 aligned with PRZN_SERME | P07268 from UniProtKB/Swiss-Prot  Length:487

    Alignment length:468
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479        
           PRZN_SERME    20 TGYDAVDDLLHYHERGNGIQINGKDSFSNEQAGLFITRENQTWNGYKVFGQPVKLTFSFPDYKFSSTNVAGDTGLSKFSAEQQQQAKLSLQSWADVANITFTEVAAGQKANITFGNYSQDRPGHYDYGTQAYAFLPNTIWQGQDLGGQTWYNVNQSNVKHPATEDYGRQTFTHEIGHALGLSHPGDYNAGEGNPTYRDVTYAEDTRQFSLMSYWSETNTGGDNGGHYAAAPLLDDIAAIQHLYGANLSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTANQRINLNEKSFSDVGGLKGNVSIAAGVTIENAIGGSGNDVIVGNAANNVLKGGAGNDVLFGGGGADELWGGAGKDIFVFSAASDSAPGASDWIRDFQKGIDKIDLSFFNKEAQSSDFIHFVDHFSGAAGEALLSYNASNNVTDLSVNIGGHQAPDFLVKIVGQVDVATDFIV 487
               SCOP domains d1srpa2 A:4-246 Metalloprotease                                                                                                                                                                                                                    d1srpa1 A:247-471 Metalloprotease                                                                                                                                                                                                 SCOP domains
               CATH domains 1srpA01       1srpA02 A:18-250 Collagenase (Catalytic Domain)                                                                                                                                                                                          1srpA01 A:4-17,A:251-471 Alkaline Protease, subunit P, domain 1                                                                                                                                                               CATH domains
           Pfam domains (1) ---------------------------------------------------------------Peptidase_M10-1srpA01 A:67-209                                                                                                                 -----------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1s----------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_M10_C-1srpA06 A:248-471                                                                                                                                                                                                Pfam domains (5)
         Sec.struct. author .hhhhhhhhh..................hhhhhhhh................eeeeee.....................hhhhhhhhhhhhhhhhh..eeeee........eeeeee.............eee..............eeeee...hhhh.....hhhhhhhhhhhhhhh.....................................................hhhhhhhhhhh...........eeee...................eee.......eee........eee.....eee.......eee.......eee......eee......eee......eee......eee......eee............eee........eee.hhhhhhh......ee.........eeeeeee....eeeeee.........eeeeee........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOLYSIN_CALCIUM  ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1srp A   4 TGYDAVDDLLHYHERGNGIQINGKDSFSNEQAGLFITRENQTWNGYKVFGQPVKLTFSFPDYKFSSTNVAGDTGLSKFSAEQQQQAKLSLQSWADVANITFTEVAAGQKANITFGNYSQDRPGHYDYGTQAYAFLPNTIWQGQDLGGQTWYNVNQSNVKHPATEDYGRQTFTHEIGHALGLSHPGDYNAGEGNPTYRDVTYAEDTRQFSLMSYWSETNTGGDNGGHYAAAPLLDDIAAIQHLYGANLSTRTGDTVYGFNSNTGRDFLSTTSNSQKVIFAAWDAGGNDTFDFSGYTANQRINLNEKSFSDVGGLKGNVSIAAGVTIENAIGGSGNDVIVGNAANNVLKGGAGNDVLFGGGGADELWGGAGKDIFVFSAASDSAPGASDWIRDFQKGIDKIDLSFFNKEAQSSDFIHFVDHFSGAAGEALLSYNASNNVTDLSVNIGGHQAPDFLVKIVGQVDVATDFIV 471
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463

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: 3-Layer(aba) Sandwich (12045)

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

E-15 (Serratia sp) (1)

1srpA02

A:18-250

Class: Mainly Beta (13760)

Architecture: 2 Solenoid (23)

Topology: Alkaline Protease, subunit P, domain 1 (23)

Homologous Superfamily: Alkaline Protease, subunit P, domain 1 (23)

E-15 (Serratia sp) (1)

1srpA01

A:4-17,A:251-471

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PRZN_SERME | P07268)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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