Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  THE CRYSTAL STRUCTURE OF METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII IN COMPLEX WITH L-CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE
 
Authors :  S. V. Revtovich, A. D. Nikulin, E. A. Morozova, T. V. Demidkina
Date :  27 Jan 14  (Deposition) - 26 Nov 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Aminotransferase Class I And Ii, Methionine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. A. Kuznetsov, N. G. Faleev, A. A. Kuznetsova, E. A. Morozova, S. V. Revtovich, N. V. Anufrieva, A. D. Nikulin, O. S. Fedorova, T. V. Demidkina
Pre-Steady-State Kinetic And Structural Analysis Of Interaction Of Methionine Gamma-Lyase From Citrobacter Freundii With Inhibitors.
J. Biol. Chem. V. 290 671 2015
PubMed-ID: 25398880  |  Reference-DOI: 10.1074/JBC.M114.586511

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    Chains: A
    EC Number: 4.4.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: H922_06139, MEGL
    Organism Scientific: CITROBACTER FREUNDII
    Organism Taxid: 546

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2LCS1Ligand/Ion[5-HYDROXY-6-METHYL-4-({[(4E)-3-OXO-1,2-OXAZOLIDIN-4-YLIDENE]AMINO}METHYL)PYRIDIN-3-YL]METHYL DIHYDROGENPHOSPHATE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LCS4Ligand/Ion[5-HYDROXY-6-METHYL-4-({[(4E)-3-OXO-1,2-OXAZOLIDIN-4-YLIDENE]AMINO}METHYL)PYRIDIN-3-YL]METHYL DIHYDROGENPHOSPHATE
3PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE8Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:58 , ARG A:60 , SER A:87 , GLY A:88 , ILE A:89 , TYR A:113 , ASP A:185 , THR A:187 , SER A:207 , THR A:209 , LYS A:210 , VAL A:338 , SER A:339 , LEU A:340 , ARG A:374 , HOH A:685BINDING SITE FOR RESIDUE LCS A 401
2AC2SOFTWAREPRO A:191 , TYR A:192 , GLN A:303 , GLN A:305 , SER A:307 , HOH A:676BINDING SITE FOR RESIDUE PGE A 402
3AC3SOFTWAREGLU A:270 , LYS A:274 , GLU A:383 , HOH A:627BINDING SITE FOR RESIDUE PGE A 403
4AC4SOFTWAREARG A:277 , GLU A:280 , GLY A:292 , LEU A:293 , SER A:294 , SER A:295BINDING SITE FOR RESIDUE PEG A 404
5AC5SOFTWAREPHE A:9 , TYR A:192 , GLU A:266 , SER A:307 , HOH A:665 , HOH A:745BINDING SITE FOR RESIDUE PEG A 405
6AC6SOFTWAREASN A:271 , GLY A:378 , GLU A:380 , ILE A:385BINDING SITE FOR RESIDUE CL A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OMA)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:157 -Pro A:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OMA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OMA)

(-) Exons   (0, 0)

(no "Exon" information available for 4OMA)

(-) Sequences/Alignments

Asymmetric 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:396
                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh........................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhh.....ee.........eee..........hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4oma A   2 SDCRTYGFNTQIVHAGQQPDPSTGALSTPIFQTSTFVFDSAEQGAARFALEESGYIYTRLGNPTTDALEKKLAVLERGEAGLATASGISAITTTLLTLCQQGDHIVSASAIYGCTHAFLSHSMPKFGINVSFVDAAKPEEIRAAMRPETKVVYIETPANPTLSLVDIETVAGIAHQQGALLVVDNTFMSPYCQQPLQLGADIVVHSVTKYINGHGDVIGGIIVGKQEFIDQARFVGLKDITGGCMSPFNAWLTLRGVKTLGIRMERHCENALKIARFLEGHPSITRVYYPGLSSHPQYELGQRQMSLPGGIISFEIAGGLEAGRRMINSVELCLLAVSLGDTETLIQHPASMTHSPVAPEERLKAGITDGLIRLSVGLEDPEDIINDLEHAIRKAT 397
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391
   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 4OMA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OMA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OMA)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LCS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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 ]
 
  Cis Peptide Bonds
    Thr A:157 - Pro A:158   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4oma
    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
  Q84AR1_CITFR | Q84AR1
    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
  Q84AR1_CITFR | Q84AR1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q84AR1_CITFR | Q84AR1: 1y4i 2rfv 3jw9 3jwa 3jwb 3mkj 4hf8 4mkj 4mkk

(-) Related Entries Specified in the PDB File

1d7u CRYSTAL STRUCTURE OF THE 2,2-DIALKYLGLYCINE DECARBOXYLASE IN COMPLEX WITH L-CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE
2daa CRYSTAL STRUCTURE OF THE D-AMINO ACID AMINOTRANSFERASE IN COMPLEX WITH D-CYCLOSERINE PYRIDOXAL-5'-PHOSPHATE
2rfv HIGH RESOLUTION STRUCTURE OF THE L-METHIONINE GAMMA-LYASE HOLOENZYME
4hf8 CRYSTAL STRUCTURE OF L-METHIONINE GAMMA-LYASE IN COMPLEX WITH GLYCINE PYRIDOXAL-5'-PHOSPHATE