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 :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGMATINE DEIMINASE FROM CELL FREE EXPRESSION
 
Authors :  E. S. Burgie, C. A. Bingman, G. N. Phillips Jr. , Center For Eukaryotic Structural Genomics (Cesg)
Date :  24 Apr 09  (Deposition) - 26 May 09  (Release) - 18 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  X
Keywords :  Agmatine, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, N- Carbamoylputrescine, Arginine Decarboxylase Pathway, Hydrolase, Polyamine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Burgie, C. A. Bingman, G. N. Phillips Jr.
Structural Insights Into The Catalytic Mechanism Of Arabidopsis Thaliana Agmatine Deiminase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGMATINE DEIMINASE
    Chains: X
    EC Number: 3.5.3.12
    Engineered: YES
    Expression System: CELL-FREE SYNTHESIS
    Expression System Plasmid: PEU-HIS-FLEXI
    Expression System Vector Type: PLASMID
    Gene: AIH, AT5G08170, EMB1873, T22D6.110
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Other Details: WHEAT GERM
    Strain: COLUMBIA
    Synonym: AGMATINE IMINOHYDROLASE, PROTEIN EMBRYO DEFECTIVE 1873

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
22111Ligand/Ion2,2',2''-NITRILOTRIETHANOL
3CL2Ligand/IonCHLORIDE ION
4K1Ligand/IonPOTASSIUM ION
5MG1Ligand/IonMAGNESIUM ION
6MSE7Mod. Amino AcidSELENOMETHIONINE
7NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS X:52 , GLY X:350BINDING SITE FOR RESIDUE CL X 384
2AC2SOFTWAREARG X:144 , ARG X:154BINDING SITE FOR RESIDUE CL X 385
3AC3SOFTWAREASP X:119 , TRP X:120 , SER X:143 , HOH X:461 , HOH X:581 , HOH X:606BINDING SITE FOR RESIDUE MG X 386
4AC4SOFTWAREARG X:73 , LYS X:74 , LEU X:76 , HOH X:480 , HOH X:493 , HOH X:723BINDING SITE FOR RESIDUE NA X 387
5AC5SOFTWARE1PE X:391BINDING SITE FOR RESIDUE NA X 388
6AC6SOFTWARETRP X:125 , ASP X:130 , ASP X:220 , ASN X:222 , HOH X:555 , HOH X:710BINDING SITE FOR RESIDUE K X 389
7AC7SOFTWAREASN X:35 , TRP X:91 , ASP X:94 , TRP X:125 , CYS X:132 , ASP X:220 , THR X:221 , ARG X:301 , ALA X:360 , GLY X:361 , HOH X:526 , HOH X:558BINDING SITE FOR RESIDUE 211 X 390
8AC8SOFTWAREASP X:265 , TYR X:283 , MSE X:284 , GLU X:286 , GLY X:304 , NA X:388BINDING SITE FOR RESIDUE 1PE X 391

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H7C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H7C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H7C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H7C)

(-) Exons   (0, 0)

(no "Exon" information available for 3H7C)

(-) 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 X from PDB  Type:PROTEIN  Length:369
 aligned with AGUA_ARATH | Q8GWW7 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:376
                                    10        20        30        40        50        60        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      
           AGUA_ARATH     1 MEESRESPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFADVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRPVKLSSLNRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
               SCOP domains d3h7cx_ X: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3h7cX00 X:1-376 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.........eeeeee.........hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh....eeee......hhhhhh.eeee...-------...eeeeeee....hhhhhh......hhhhhhhhhhhhhh..eeeeeee.hhh.eee....eeeeehhhhh........hhhhhhhhhhhhhh..eeeee......hhhhh.hhhh.eeeee..eeeeee......hhhhhhhhhhhhhhh.........eeeeee.......hhhhhhh.......................eee..eeeee.....hhhhhhhhhhhhhh...eeeee..hhhhhh...hhhhheeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h7c X   1 SEESRESPAEHGYYmPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEmSmNDSWFRDSGPTFIVRKR-------NRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSmILEGGSIHVDGEGTCLVTEECLLNKNRNPHmSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNmCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYmTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
                                    10    |   20        30        40        50        60        70        80    | | 90       100   |     - |     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      
                                         15-MSE                                                                85-MSE            104     112                                            159-MSE                        190-MSE                               228-MSE                                                 284-MSE                                                                                        
                                                                                                                 87-MSE
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H7C)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (AGUA_ARATH | Q8GWW7)
molecular function
    GO:0047632    agmatine deiminase activity    Catalysis of the reaction: agmatine + H2O = N-carbamoylputrescine + NH3.
    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:0004668    protein-arginine deiminase activity    Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3.
biological process
    GO:0006596    polyamine biosynthetic process    The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
    GO:0009446    putrescine biosynthetic process    The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane; putrescine can be synthesized from arginine or ornithine and is the metabolic precursor of spermidine and spermine.
    GO:0033388    putrescine biosynthetic process from arginine    The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine.

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    211  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3h7c)
 

(-) 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
  3h7c
    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
  AGUA_ARATH | Q8GWW7
    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)
  3.5.3.12
    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
  AGUA_ARATH | Q8GWW7
    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
        AGUA_ARATH | Q8GWW7: 1vkp 2q3u 3h7k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3H7C)