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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   PRTC METHIONINE MUTANTS: M226A_DESY

Authors :   A. E. Oberholzer, M. Bumann, T. Hege, S. Russo, U. Baumann

Date :   07 May 09 (Deposition) - 30 Jun 09 (Release) - 17 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.13

Chains :   Asym./Biol. Unit : P,Z

Keywords :   Met-Turn, Beta Roll, Metalloprotease, Metzincin, Hydrolase, Metal- Binding, Protease, Secreted, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. E. Oberholzer, M. Bumann, T. Hege, S. Russo, U. Baumann
Metzincin'S Canonical Methionine Is Responsible For The Structural Integrity Of The Zinc-Binding Site
Biol. Chem. V. 390 875 2009
PubMed-ID: 19558324 | Reference-DOI: 10.1515/BC.2009.100

Molecule 1 - SECRETED PROTEASE C
	Chains	:	P
	EC Number	:	3.4.24.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC18 DERIVATIVE
	Expression System Strain	:	XL1BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PRTC
	Mutation	:	YES
	Organism Scientific	:	ERWINIA CHRYSANTHEMI
	Organism Taxid	:	556
	Synonym	:	PROC

Molecule 2 - UNCHARACTERIZED PEPTIDE
	Chains	:	Z
	Engineered	:	YES
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	P	Z

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 9)

No.	Name	Count	Type	Full Name
1	CA	7	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG P:265 , GLY P:267 , SER P:269 , ASP P:297 , GLY P:299 , ASP P:302	BINDING SITE FOR RESIDUE CA P 480
2	AC2	SOFTWARE	GLY P:300 , ASP P:302 , THR P:339 , GLU P:341 , HOH P:634 , HOH P:635	BINDING SITE FOR RESIDUE CA P 481
3	AC3	SOFTWARE	GLY P:346 , GLY P:348 , ASP P:350 , GLY P:363 , ALA P:365 , ASP P:368	BINDING SITE FOR RESIDUE CA P 482
4	AC4	SOFTWARE	ASN P:355 , ALA P:357 , ASN P:359 , GLY P:372 , ALA P:374 , ASP P:377	BINDING SITE FOR RESIDUE CA P 483
5	AC5	SOFTWARE	GLY P:364 , GLY P:366 , ASP P:368 , GLY P:381 , ALA P:383 , ASP P:386	BINDING SITE FOR RESIDUE CA P 484
6	AC6	SOFTWARE	HOH P:10 , GLY P:382 , GLY P:384 , ASP P:386 , GLN P:408 , ASP P:412	BINDING SITE FOR RESIDUE CA P 485
7	AC7	SOFTWARE	GLY P:373 , GLY P:375 , ASP P:377 , ASP P:395 , ASP P:402 , HOH P:636	BINDING SITE FOR RESIDUE CA P 487
8	AC8	SOFTWARE	ARG P:265 , GLY P:267 , SER P:269 , HOH P:659	BINDING SITE FOR RESIDUE CL P 1
9	AC9	SOFTWARE	GLN P:110 , SER P:113 , HOH P:508 , HOH P:694	BINDING SITE FOR RESIDUE CL P 3

(no "SS Bond" information available for 3HDA)

(no "Cis Peptide Bond" information available for 3HDA)

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

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.	PRTC_DICCH	185-194	1	P:185-194
2	HEMOLYSIN_CALCIUM	PS00330	Hemolysin-type calcium-binding region signature.	PRTC_DICCH	368-386	1	P:368-386

(no "Exon" information available for 3HDA)

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 P from PDB  Type:PROTEIN  Length:382
 aligned with PRTC_DICCH | P16317 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:419
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         
           PRTC_DICCH    61 NVSWNGTNVFGKSANLTFKFLQSVSSIPSGDTGFVKFNAEQIEQAKLSLQSWSDVANLTFTEVTGNKSANITFGNYTRDASGNLDYGTQAYAYYPGNYQGAGSSWYNYNQSNIRNPGSEEYGRQTFTHEIGHALGLAHPGEYNAGEGDPSYNDAVYAEDSYQFSIMSYWGENETGADYNGHYGGAPMIDDIAAIQRLYGANMTTRTGDSVYGFNSNTDRDFYTATDSSKALIFSVWDAGGTDTFDFSGYSNNQRINLNEGSFSDVGGLKGNVSIAHGVTIENAIGGSGNDILVGNSADNILQGGAGNDVLYGGAGADTLYGGAGRDTFVYGSGQDSTVAAYDWIADFQKGIDKIDLSAFRNEGQLSFVQDQFTGKGQEVMLQWDAANSITNLWLHEAGHSSVDFLVRIVGQAAQSDIIV 479
               SCOP domains d3hdap2 P:61-258 Metalloprotease                                                                                                                                                                      d3hdap1 P:259-479 Metalloprotease                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..ee......eeeeeee.................hhhhhhhhhhhhhhhhh...eeeee........eeeeee.............eeee.........eeeee..hhhhhh...hhhhhhhhhhhhhhhh......-------------------------------------.........hhhhhhhhhhhhh..........eeee.....hhh.ee........eee.......eee........eee.....ee........eee.......eee......eee......eee......eee......eee......eee..hhhhhhhhhheee........eee.hhhhhhh..ee..........eeeeeee....eeeeeee........eeeeee...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOLYSIN_CALCIUM  --------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hda P  61 NVSWNGTNVFGKSANLTFKFLQSVSSIPSGDTGFVKFNAEQIEQAKLSLQSWSDVANLTFTEVTGNKSANITFGNYTRDASGNLDYGTQAYAYYPGNYQGAGSSWYNYNQSNIRNPGSEEYGRQTFTHEIGHALGLAHPG-------------------------------------YNGHYGGAPMIDDIAAIQRLYGANMTTRTGDSVYGFNSNTDRDFYTATDSSKALIFSVWDAGGTDTFDFSGYSNNQRINLNEGSFSDVGGLKGNVSIAHGVTIENAIGGSGNDILVGNSADNILQGGAGNDVLYGGAGADTLYGGAGRDTFVYGSGQDSTVAAYDWIADFQKGIDKIDLSAFRNEGQLSFVQDQFTGKGQEVMLQWDAANSITNLWLHEAGHSSVDFLVRIVGQAAQSDIIV 479
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200         -         -         -       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         
                                                                                                                                                                     200                                   238

Chain Z from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author .eeee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3hda Z   1 AEAAQA   6

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 '\|'

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (PRTC_DICCH | P16317)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hda)

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	3hda
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	3.4.24.-
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	PRTC_DICCH \| P16317	:	1go7 1go8 1k7g 1k7i 1k7q 3hb2 3hbu 3hbv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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