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 :  REACTION INTERMEDIATE STRUCTURE OF ENTAMOEBA HISTOLYTICA METHIONINE GAMMA-LYASE 1 CONTAINING ALPHA-AMINO-ALPHA, BETA-BUTENOIC ACID-PYRIDOXAL-5'-PHOSPHATE
 
Authors :  T. Karaki, D. Sato, A. Shimizu, T. Nozaki, S. Harada
Date :  10 Feb 10  (Deposition) - 09 Feb 11  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Gamma-Lyase, L-Methionine, Entamoeba Histolytica, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Karaki, D. Sato, A. Shimizu, T. Nozaki, S. Harada
Crystal Structure Of Entamoeba Histolytica Methionine Gamma-Lyase 1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    Chains: A, B, C, D
    EC Number: 4.4.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector: PGEX6P1
    Expression System Vector Type: VECTOR
    Gene: METG
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
14LM4Ligand/Ion(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC ACID
2GOL2Ligand/IonGLYCEROL
3MEE2Ligand/IonMETHANETHIOL
4SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:82 , GLY A:83 , MET A:84 , TYR A:108 , ASN A:155 , ASP A:180 , SER A:202 , SER A:204 , LYS A:205 , SER A:332 , THR A:347 , ARG A:367 , MEE A:2002 , TYR D:1553 , ARG D:1555BINDING SITE FOR RESIDUE 4LM A 2001
02AC2SOFTWARETYR A:108 , THR A:347 , 4LM A:2001BINDING SITE FOR RESIDUE MEE A 2002
03AC3SOFTWARESER B:582 , GLY B:583 , MET B:584 , TYR B:608 , GLU B:651 , ASN B:655 , ASP B:680 , THR B:682 , SER B:702 , SER B:704 , LYS B:705 , ILE B:714 , SER B:832 , THR B:847 , ARG B:867 , TYR C:1053 , ARG C:1055BINDING SITE FOR RESIDUE 4LM B 2003
04AC4SOFTWARETYR B:553 , ARG B:555 , SER C:1082 , GLY C:1083 , MET C:1084 , TYR C:1108 , ASN C:1155 , ASP C:1180 , THR C:1182 , SER C:1202 , SER C:1204 , LYS C:1205 , GLY C:1215 , SER C:1332 , LEU C:1333 , THR C:1347 , ARG C:1367 , MEE C:2005BINDING SITE FOR RESIDUE 4LM C 2004
05AC5SOFTWARETYR C:1108 , 4LM C:2004BINDING SITE FOR RESIDUE MEE C 2005
06AC6SOFTWARETYR A:53 , ARG A:55 , SER D:1582 , GLY D:1583 , MET D:1584 , TYR D:1608 , ASN D:1655 , ASP D:1680 , THR D:1682 , SER D:1702 , SER D:1704 , LYS D:1705 , ILE D:1714 , GLY D:1715 , SER D:1832 , THR D:1847 , ARG D:1867BINDING SITE FOR RESIDUE 4LM D 2006
07AC7SOFTWAREARG A:176 , HOH A:3655BINDING SITE FOR RESIDUE SO4 A 2007
08AC8SOFTWAREARG B:676 , HOH B:3630BINDING SITE FOR RESIDUE SO4 B 2008
09AC9SOFTWAREARG C:1176 , HOH C:3423 , HOH C:3664BINDING SITE FOR RESIDUE SO4 C 2009
10BC1SOFTWAREARG D:1676 , HOH D:3248BINDING SITE FOR RESIDUE SO4 D 2010
11BC2SOFTWARELYS A:312 , HOH A:3124BINDING SITE FOR RESIDUE GOL A 2011
12BC3SOFTWAREHOH C:3564 , HOH C:3592BINDING SITE FOR RESIDUE GOL C 2012

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:152 -Pro A:153
2Asn A:155 -Pro A:156
3Ser B:652 -Pro B:653
4Asn B:655 -Pro B:656
5Ser C:1152 -Pro C:1153
6Asn C:1155 -Pro C:1156
7Ser D:1652 -Pro D:1653
8Asn D:1655 -Pro D:1656

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AEP)

(-) Exons   (0, 0)

(no "Exon" information available for 3AEP)

(-) 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:387
 aligned with Q86D28_ENTHI | Q86D28 from UniProtKB/TrEMBL  Length:389

    Alignment length:387
                                    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       
        Q86D28_ENTHI      3 AQDITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFSFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALELW  389
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.......................hhhhhhhhhhh...........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhh....eeeeeee..........hhhhhhhhhhhhh.eeeee.........hhhhhh..eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhh.....ee.........eeehhhhh.....hhhhhhhhh....eeeee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3aep A    3 AQDITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFLFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALELW  389
                                    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       


Chain B from PDB  Type:PROTEIN  Length:386
 aligned with Q86D28_ENTHI | Q86D28 from UniProtKB/TrEMBL  Length:389

    Alignment length:386
                                    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      
        Q86D28_ENTHI      3 AQDITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFSFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALEL  388
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.......................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee.........hhhhhh..eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhh.....ee.........eeehhhhh.....hhhhhhhhh....eeeee....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3aep B  503 AQDITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFLFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALEL  888
                                   512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882      


Chain C from PDB  Type:PROTEIN  Length:387
 aligned with Q86D28_ENTHI | Q86D28 from UniProtKB/TrEMBL  Length:389

    Alignment length:387
                                    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       
        Q86D28_ENTHI      3 AQDITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFSFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALELW  389
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.......................hhhhhhhhhhh...........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhh....eeeeeee..........hhhhhhhhhhhhh.eeeee.........hhhhh...eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhh.....ee.........eee..........hhhhhhhhh....eeeee....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3aep C 1003 AQDITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFLFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALELW 1389
                                  1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382       


Chain D from PDB  Type:PROTEIN  Length:384
 aligned with Q86D28_ENTHI | Q86D28 from UniProtKB/TrEMBL  Length:389

    Alignment length:384
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384    
        Q86D28_ENTHI      5 DITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFSFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALEL  388
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh.......................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee.........hhhhhh..eeeee.............eeeee.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhh.....ee.........eeehhhhh.....hhhhhhhhh....eeeee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3aep D 1505 DITTTLLHPKGDHVLHSHAYPIFQTSTFCFDSTQQGADLFMGKGEGHIYSRLGNPTVEQFEEMVCSIEGAAGSAAFGSGMGAISSSTLAFLQKGDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEKVKAAWKPNTKMVYLESPANPTCKVSDIKGIAVVCHERGARLVVDATFTSPCFLKPLELGADIALHSVSKYINGHGDVIGGVSSAKTAEDIATIKFYRKDAGSLMAPMDAFLCARGMKTLPIRMQIHMENGLKVAKFLEQHEKIVKVNHPGLESFPGHDIAKKQMTGYGSTFLFEMKSFEAAKKLMEHLKVCTLAVSLGCVDTLIEHPASMTHAAVPENIMRKQGITPELVRISVGIENVDDIIADLKQALEL 1888
                                  1514      1524      1534      1544      1554      1564      1574      1584      1594      1604      1614      1624      1634      1644      1654      1664      1674      1684      1694      1704      1714      1724      1734      1744      1754      1764      1774      1784      1794      1804      1814      1824      1834      1844      1854      1864      1874      1884
   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  (0, 0)

(no "SCOP Domain" information available for 3AEP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q86D28_ENTHI | Q86D28)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0018826    methionine gamma-lyase activity    Catalysis of the reaction: L-methionine = methanethiol + NH3 + 2-oxobutanoate.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.

 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
    4LM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MEE  [ 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 ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:155 - Pro A:156   [ RasMol ]  
    Asn B:655 - Pro B:656   [ RasMol ]  
    Asn C:1155 - Pro C:1156   [ RasMol ]  
    Asn D:1655 - Pro D:1656   [ RasMol ]  
    Ser A:152 - Pro A:153   [ RasMol ]  
    Ser B:652 - Pro B:653   [ RasMol ]  
    Ser C:1152 - Pro C:1153   [ RasMol ]  
    Ser D:1652 - Pro D:1653   [ RasMol ]  
 

(-) 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
  3aep
    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
  Q86D28_ENTHI | Q86D28
    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)
  4.4.1.11
    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
  Q86D28_ENTHI | Q86D28
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q86D28_ENTHI | Q86D28: 3acz 3aej 3ael 3aem 3aen 3aeo

(-) Related Entries Specified in the PDB File

3acz THE SAME PROTEIN COMPLEXED WITH SUBSTRATE.
3aej
3ael
3aem
3aen
3aeo