1OM8 - 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)

Title :   CRYSTAL STRUCTURE OF A COLD ADAPTED ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18, CO-CRYSTALLYZED WITH 10 MM EDTA

Authors :   S. Ravaud, P. Gouet, R. Haser, N. Aghajari

Date :   25 Feb 03 (Deposition) - 15 Jul 03 (Release) - 07 May 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Beta Jelly Roll, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Ravaud, P. Gouet, R. Haser, N. Aghajari
Probing The Role Of Divalent Metal Ions In A Bacterial Psychrophilic Metalloprotease: Binding Studies Of An Enzyme In The Crystalline State By X-Ray Crystallography.
J. Bacteriol. V. 185 4195 2003
PubMed-ID: 12837794 | Reference-DOI: 10.1128/JB.185.14.4195-4203.2003

Molecule 1 - SERRALYSIN
	Chains	:	A
	EC Number	:	3.4.24.40
	Organism Scientific	:	PSEUDOMONAS SP. 'TAC II 18'
	Organism Taxid	:	76981
	Strain	:	TAC II 18
	Synonym	:	CALCIUM AND ZINC DEPENDENT ALKALINE PROTEASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:250 , ASP A:252 , THR A:254 , ASP A:282 , GLY A:284 , ASP A:287	BINDING SITE FOR RESIDUE CA A 701
2	AC2	SOFTWARE	GLY A:285 , THR A:324 , GLU A:326 , HOH A:1129 , HOH A:1130	BINDING SITE FOR RESIDUE CA A 702
3	AC3	SOFTWARE	GLY A:331 , GLY A:333 , ASP A:335 , GLY A:348 , ALA A:350 , ASP A:353	BINDING SITE FOR RESIDUE CA A 703
4	AC4	SOFTWARE	GLY A:349 , GLY A:351 , ASP A:353 , GLY A:366 , THR A:368 , ASP A:371	BINDING SITE FOR RESIDUE CA A 704
5	AC5	SOFTWARE	ASN A:340 , ALA A:342 , ASN A:344 , GLY A:357 , GLY A:359 , ASP A:362	BINDING SITE FOR RESIDUE CA A 705
6	AC6	SOFTWARE	GLY A:358 , GLY A:359 , GLY A:360 , ASP A:362 , ASP A:380 , ASP A:387 , HOH A:1146	BINDING SITE FOR RESIDUE CA A 706
7	AC7	SOFTWARE	ARG A:139 , TRP A:210 , SER A:211 , LYS A:213 , ASN A:214 , HOH A:1056 , HOH A:1119 , HOH A:1368 , HOH A:1402	BINDING SITE FOR RESIDUE SO4 A 500

(no "SS Bond" information available for 1OM8)

(no "Cis Peptide Bond" information available for 1OM8)

(no "SAP(SNP)/Variant" information available for 1OM8)

(no "PROSITE Motif" information available for 1OM8)

(no "Exon" information available for 1OM8)

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:452
 aligned with O69771_9PSED | O69771 from UniProtKB/TrEMBL  Length:480

    Alignment length:461
                                    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 
         O69771_9PSED    20 GTSSAFTQIDNFSHFYDRGEHLVNGKPSFTVDQVADQLTRSGASWHDLNNDGVINLTYTFLTAPPVGYASRGLGTFSQFSALQKEQAKLSLESWADVAKVTFTEGPAARGDDGHMTFANFSASNGGAAFAYLPNSSRKGESWYLINKDYQVNKTPGEGNYGRQTLTHEIGHTLGLSHPGDYNAGNGNPTYRDAVYAEDTRAYSVMSYWSEKNTGQVFTKTGEGAYASAPLLDDIAAVQKLYGANLETRADDTVYGFNSTADRDFYSATSSTDKLIFSVWDGGGNDTLDFSGFSQNQKINLTAGSFSDVGGMTGNVSIAQGVTIENAIGGSGNDLLIGNDAANVLKGGAGNDIIYGGGGADVLWGGTGSDTFVFGAVSDSTPKAADIIKDFQSGFDKIDLTAITKLGGLNFVDAFTGHAGDAIVSYHQASNAGSLQVDFSGQGVADFLVTTVGQVATYDIVA 480
               SCOP domains d1om8a2 A:3-244 Metalloprotease                                                                                                                                                                                                                   d1om8a1 A:245-463 Metalloprotease                                                                                                                                                                                           SCOP domains
               CATH domains 1om8A01          1om8A02 A:20-247 Collagenase (  Catalytic Domain)                                                                                                                                                                                   1om8A01 A:3-19,A:248-460 Alkaline Protease, subunit P, domain 1                                                                                                                                                      --- CATH domains
           Pfam domains (1) -----------------------------------------------  --------------------------Reprolysin_2-1om8A01 A:78-223                                                                                                                     ------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1o-------------------------------------------------------- --------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1o------------------------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1o------------------------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) -----------------------------------------------  -----------------------------------------------------------------------------------------------------------------------------------      --------------------------------------------------------Peptidase_M10_C-1om8A05 A:245-463                                                                                                                                                                                           Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhh......ee..ee..hhhhhhhhhh........--....eeeeeee......hhhhhh.......hhhhhhhhhhhhhhhhhhh.eeeee........eeeeeeee.hhhhh.eee.........eeeee.....hhhhh....hhhhhhhhhhhhhhhh......------..hhhhh...............hhhhhh...............hhhhhhhhhhhhh..........eeee.....hhh.ee........eee.......eee........eee.....ee........eee.......eee......eee......eee......eee......eee......eee..hhhhhhhhhheee........eeehhhhhh....ee.........eeeeeee.-..eeeeeee........eeeeee...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1om8 A   3 GTSSAFTQIDNFSHFYDRGDHLVNGKPSFTVDQVADQLTRSGASWHD--NDGVINLTYTFLTAPPVGYASRGLGTFSQFSALQKEQAKLSLESWADVAKVTFTEGPAARGDDGHMTFANFSASNGGAAFAYLPNSSRKGESWYLINKDYQVNKTPGEGNYGRQTLTHEIGHTLGLSHPGD------NPTYRDAVYAEDTRAYSVMSYWSEKNTGQVFTKTGEGAYASAPLLDDIAAVQKLYGANLETRADDTVYGFNSTADRDFYSATSSTDKLIFSVWDGGGNDTLDFSGFSQNQKINLTAGSFSDVGGMTGNVSIAQGVTIENAIGGSGNDLLIGNDAANVLKGGAGNDIIYGGGGADVLWGGTGSDTFVFGAVSDSTPKAADIIKDFQSGFDKIDLTAITKLGGLNFVDAFTGHAGDAIVSYHQ-SNAGSLQVDFSGQGVADFLVTTVGQVATYDIVA 463
                                    12        22        32        42      | 52        62        72        82        92       102       112       122       132       142       152       162       172       182      |192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422      |432       442       452       462 
                                                                         49 52                                                                                                                               182    189                                                                                                                                                                                                                                             429 |                                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      431

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(

)

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)

'tac ii 18' (Pseudomonas sp) (6)

1om8A02

A:20-247

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)

'tac ii 18' (Pseudomonas sp) (6)

1om8A01

A:3-19,A:248-460

Asymmetric Unit(hide GO term definitions)

Chain A (O69771_9PSED | O69771)

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: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: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 Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1om8)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1om8
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	O69771_9PSED \| O69771
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	3.4.24.40
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	O69771_9PSED \| O69771
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	O69771_9PSED \| O69771	:	1g9k 1h71 1o0q 1o0t 1om6 1om7 1omj

1g9k	CRYSTAL STRUCTURE OF A COLD ADAPTED ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18, NATIVE STATE, RHOMBOHEDRAL FORM
1h71	CRYSTAL STRUCTURE OF A COLD ADAPTED ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18, NATIVE STATE, ORTHORHOMBIC FORM
1kap	CRYSTAL STRUCTURE OF A MESOPHILIC ALKALINE PROTEASE FROM PSEUDOMONAS AERUGINOSA
1o0q
1o0t
1om6
1om7
1omj
1smp	CRYSTAL STRUCTURE OF THE MESOPHILIC SERRATIA PROTEASE FROM SERRATIA MARCESCENS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (3, 5)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File