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(-) Description

Title :  PRTC FROM ERWINIA CHRYSANTHEMI: Y228F MUTANT
 
Authors :  U. Baumann, T. Hege
Date :  19 Oct 01  (Deposition) - 19 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Metalloprotease, Hydrolase, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hege, U. Baumann
Protease C Of Erwinia Chrysanthemi: The Crystal Structure And Role Of Amino Acids Y228 And E189
J. Mol. Biol. V. 314 187 2001
PubMed-ID: 11718553  |  Reference-DOI: 10.1006/JMBI.2001.5124
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SECRETED PROTEASE C
    Chains: A
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRTC
    Mutation: YES
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556
    Synonym: PROC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:265 , GLY A:267 , SER A:269 , ASP A:297 , GLY A:299 , ASP A:302BINDING SITE FOR RESIDUE CA A 480
2AC2SOFTWAREGLY A:300 , ASP A:302 , THR A:339 , GLU A:341 , HOH A:653 , HOH A:797BINDING SITE FOR RESIDUE CA A 481
3AC3SOFTWAREGLY A:346 , GLY A:348 , ASP A:350 , GLY A:363 , ALA A:365 , ASP A:368BINDING SITE FOR RESIDUE CA A 482
4AC4SOFTWAREASN A:355 , ALA A:357 , ASN A:359 , GLY A:372 , ALA A:374 , ASP A:377BINDING SITE FOR RESIDUE CA A 483
5AC5SOFTWAREGLY A:364 , GLY A:366 , ASP A:368 , GLY A:381 , ALA A:383 , ASP A:386BINDING SITE FOR RESIDUE CA A 484
6AC6SOFTWAREGLY A:382 , GLY A:384 , ASP A:386 , GLN A:408 , ASP A:412 , HOH A:505BINDING SITE FOR RESIDUE CA A 485
7AC7SOFTWAREHIS A:188 , HIS A:192 , HIS A:198 , HOH A:798BINDING SITE FOR RESIDUE ZN A 486
8AC8SOFTWAREGLY A:373 , GLY A:375 , ASP A:377 , ASP A:395 , ASP A:402 , HOH A:534BINDING SITE FOR RESIDUE CA A 487

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K7I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K7I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K7I)

(-) PROSITE Motifs  (2, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1K7I)

(-) 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:462
 aligned with PRTC_DICCH | P16317 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:462
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477  
           PRTC_DICCH    18 ANTSSAYNSVYDFLRYHDRGDGLTVNGKTSYSIDQAAAQITRENVSWNGTNVFGKSANLTFKFLQSVSSIPSGDTGFVKFNAEQIEQAKLSLQSWSDVANLTFTEVTGNKSANITFGNYTRDASGNLDYGTQAYAYYPGNYQGAGSSWYNYNQSNIRNPGSEEYGRQTFTHEIGHALGLAHPGEYNAGEGDPSYNDAVYAEDSYQFSIMSYWGENETGADYNGHYGGAPMIDDIAAIQRLYGANMTTRTGDSVYGFNSNTDRDFYTATDSSKALIFSVWDAGGTDTFDFSGYSNNQRINLNEGSFSDVGGLKGNVSIAHGVTIENAIGGSGNDILVGNSADNILQGGAGNDVLYGGAGADTLYGGAGRDTFVYGSGQDSTVAAYDWIADFQKGIDKIDLSAFRNEGQLSFVQDQFTGKGQEVMLQWDAANSITNLWLHEAGHSSVDFLVRIVGQAAQSDIIV 479
               SCOP domains d1k7ia2 A:18-258 Metalloprotease                                                                                                                                                                                                                 d1k7ia1 A:259-479 Metalloprotease                                                                                                                                                                                             SCOP domains
               CATH domains -1k7iA01          1k7iA02 A:36-262 Collagenase (Catalytic Domain)                                                                                                                                                                                    1k7iA01 A:19-35,A:263-479 Alkaline Protease, subunit P, domain 1                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.........ee..ee..hhhhhhhhhh...ee..ee......eeeeeee.................hhhhhhhhhhhhhhhhh...eeeee........eeeeee.............eee..........eeeee..hhhhhh...hhhhhhhhhhhhhhhh...............hhhhh...............hhhhhh...........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
                 1k7i A  18 ANTSSAYNSVYDFLRYHDRGDGLTVNGKTSYSIDQAAAQITRENVSWNGTNVFGKSANLTFKFLQSVSSIPSGDTGFVKFNAEQIEQAKLSLQSWSDVANLTFTEVTGNKSANITFGNYTRDASGNLDYGTQAYAYYPGNYQGAGSSWYNYNQSNIRNPGSEEYGRQTFTHEIGHALGLAHPGEYNAGEGDPSYNDAVYAEDSYQFSIMSFWGENETGADYNGHYGGAPMIDDIAAIQRLYGANMTTRTGDSVYGFNSNTDRDFYTATDSSKALIFSVWDAGGTDTFDFSGYSNNQRINLNEGSFSDVGGLKGNVSIAHGVTIENAIGGSGNDILVGNSADNILQGGAGNDVLYGGAGADTLYGGAGRDTFVYGSGQDSTVAAYDWIADFQKGIDKIDLSAFRNEGQLSFVQDQFTGKGQEVMLQWDAANSITNLWLHEAGHSSVDFLVRIVGQAAQSDIIV 479
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477
   Legend:   → Mismatch (orange background)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1K7I)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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