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(-) Description

Title :  PRTC METHIONINE MUTANTS: M226A IN-HOUSE
 
Authors :  A. E. Oberholzer, M. Bumann, T. Hege, S. Russo, U. Baumann
Date :  05 May 09  (Deposition) - 30 Jun 09  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  P,Z
Keywords :  Met-Turn, Beta Roll, Zinc, Metalloprotease, Metzincin, Calcium, 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
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : PZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG P:265 , GLY P:267 , SER P:269 , ASP P:297 , GLY P:299 , ASP P:302BINDING SITE FOR RESIDUE CA P 480
02AC2SOFTWAREGLY P:300 , ASP P:302 , THR P:339 , GLU P:341 , HOH P:936 , HOH P:937BINDING SITE FOR RESIDUE CA P 481
03AC3SOFTWAREGLY P:346 , GLY P:348 , ASP P:350 , GLY P:363 , ALA P:365 , ASP P:368BINDING SITE FOR RESIDUE CA P 482
04AC4SOFTWAREASN P:355 , ALA P:357 , ASN P:359 , GLY P:372 , ALA P:374 , ASP P:377BINDING SITE FOR RESIDUE CA P 483
05AC5SOFTWAREGLY P:364 , GLY P:366 , ASP P:368 , GLY P:381 , ALA P:383 , ASP P:386BINDING SITE FOR RESIDUE CA P 484
06AC6SOFTWAREHOH P:12 , GLY P:382 , GLY P:384 , ASP P:386 , GLN P:408 , ASP P:412BINDING SITE FOR RESIDUE CA P 485
07AC7SOFTWAREHIS P:188 , HIS P:192 , HIS P:198 , HOH P:960BINDING SITE FOR RESIDUE ZN P 486
08AC8SOFTWAREGLY P:373 , GLY P:375 , ASP P:377 , ASP P:395 , ASP P:402 , HOH P:938BINDING SITE FOR RESIDUE CA P 487
09AC9SOFTWAREGLU P:180 , HIS P:241 , HOH P:746 , HOH P:899BINDING SITE FOR RESIDUE ZN P 488
10BC1SOFTWAREASN P:355 , SER P:356 , ALA P:374 , HOH P:799 , HOH P:821 , HOH P:874BINDING SITE FOR RESIDUE CL P 1
11BC2SOFTWARETYR P:146 , ARG P:467 , HOH P:503BINDING SITE FOR RESIDUE CL P 3
12BC3SOFTWAREGLY P:384 , GLN P:408 , HOH P:836 , HOH P:924BINDING SITE FOR RESIDUE CL P 600
13BC4SOFTWAREGLY P:366 , GLY P:384 , HOH P:840BINDING SITE FOR RESIDUE CL P 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.PRTC_DICCH185-194  1P:185-194
2HEMOLYSIN_CALCIUMPS00330 Hemolysin-type calcium-binding region signature.PRTC_DICCH368-386  1P:368-386

(-) Exons   (0, 0)

(no "Exon" information available for 3HBV)

(-) 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 P from PDB  Type:PROTEIN  Length:380
 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 d3hbvp2 P:61-258 Metalloprotease                                                                                                                                                                      d3hbvp1 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..........eee......hhhhh.........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
                 3hbv P  61 NVSWNGTNVFGKSANLTFKFLQSVSSIPSGDTGFVKFNAEQIEQAKLSLQSWSDVANLTFTEVTGNKSANITFGNYTRDASGNLDYGTQAYAYYPGNYQGAGSSWYNYNQSNIRNPGSEEYGRQTFTHEIGHALGLAH---------------------------------------YNGHYGGAPMIDDIAAIQRLYGANMTTRTGDSVYGFNSNTDRDFYTATDSSKALIFSVWDAGGTDTFDFSGYSNNQRINLNEGSFSDVGGLKGNVSIAHGVTIENAIGGSGNDILVGNSADNILQGGAGNDVLYGGAGADTLYGGAGRDTFVYGSGQDSTVAAYDWIADFQKGIDKIDLSAFRNEGQLSFVQDQFTGKGQEVMLQWDAANSITNLWLHEAGHSSVDFLVRIVGQAAQSDIIV 479
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       | -         -         -         -       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470         
                                                                                                                                                                   198                                     238                                                                                                                                                                                                                                                 


Chain Z from PDB  Type:PROTEIN  Length:7
                                       
               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
                 3hbv Z   1 AKASQAA   7
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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.

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  3hbv
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  3.4.24.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PRTC_DICCH | P16317: 1go7 1go8 1k7g 1k7i 1k7q 3hb2 3hbu 3hda

(-) Related Entries Specified in the PDB File

1go7
1go8
1k7g WILDTYPE
3hb2
3hbu
3hda