Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  PRTC METHIONINE MUTANTS: M226I
 
Authors :  A. E. Oberholzer, M. Bumann, T. Hege, S. Russo, U. Baumann
Date :  04 May 09  (Deposition) - 04 Aug 09  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  P
Keywords :  Met-Turn, Beta Roll, Hydrolase, Metal-Binding, Metalloprotease, 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

(-) 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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : P

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
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:532 , HOH P:533BINDING 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:17 , 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:556BINDING SITE FOR RESIDUE ZN P 486
08AC8SOFTWAREGLY P:373 , GLY P:375 , ASP P:377 , ASP P:395 , ASP P:402 , HOH P:535BINDING SITE FOR RESIDUE CA P 487
09AC9SOFTWAREASN P:355 , SER P:356 , ALA P:374 , HOH P:895 , HOH P:981BINDING SITE FOR RESIDUE CL P 1
10BC1SOFTWARETYR P:146 , ARG P:467 , HOH P:758BINDING SITE FOR RESIDUE CL P 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HB2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HB2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HB2)

(-) 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 3HB2)

(-) 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: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 d3hb2p1 P:18-258 Metalloprotease                                                                                                                                                                                                                 d3hb2p2 P:259-479 Metalloprotease                                                                                                                                                                                             SCOP domains
               CATH domains -3hb2P01          3hb2P02 P:36-262 Collagenase (Catalytic Domain)                                                                                                                                                                                    3hb2P01 P:19-35,P:263-479 Alkaline Protease, subunit P, domain 1                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh........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
                 3hb2 P  18 ANTSSAYNSVYDFLRYHDRGDGLTVNGKTSYSIDQAAAQITRENVSWNGTNVFGKSANLTFKFLQSVSSIPSGDTGFVKFNAEQIEQAKLSLQSWSDVANLTFTEVTGNKSANITFGNYTRDASGNLDYGTQAYAYYPGNYQGAGSSWYNYNQSNIRNPGSEEYGRQTFTHAIGHALGLAHPGEYNAGEGDPSYNDAVYAEDSYQFSIISYWGENETGADYNGHYGGAPMIDDIAAIQRLYGANMTTRTGDSVYGFNSNTDRDFYTATDSSKALIFSVWDAGGTDTFDFSGYSNNQRINLNEGSFSDVGGLKGNVSIAHGVTIENAIGGSGNDILVGNSADNILQGGAGNDVLYGGAGADTLYGGAGRDTFVYGSGQDSTVAAYDWIADFQKGIDKIDLSAFRNEGQLSFVQDQFTGKGQEVMLQWDAANSITNLWLHEAGHSSVDFLVRIVGQAAQSDIIV 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)
  - → 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  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HB2)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hb2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3hb2
    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
  PRTC_DICCH | P16317
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.-
    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

(-) Analysis Tools

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
  PRTC_DICCH | P16317
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1go7 1go8