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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA AGMATINE DEIMINASE COMPLEXED WITH A COVALENTLY BOUND REACTION INTERMEDIATE
 
Authors :  E. S. Burgie, C. A. Bingman, G. N. Phillips Jr. , Center For Eukaryoti Structural Genomics (Cesg)
Date :  27 Apr 09  (Deposition) - 26 May 09  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A
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

(-) Compounds

Molecule 1 - AGMATINE DEIMINASE
    Chains: A
    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 : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2AGT1Mod. Amino AcidS-{(S)-AMINO[(4-AMINOBUTYL)AMINO]METHYL}-L-CYSTEINE
3CL3Ligand/IonCHLORIDE ION
4MG1Ligand/IonMAGNESIUM ION
5MSE7Mod. Amino AcidSELENOMETHIONINE
6NA3Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:119 , TRP A:120 , SER A:143 , HOH A:508 , HOH A:528 , HOH A:531BINDING SITE FOR RESIDUE MG A 384
2AC2SOFTWARETRP A:125 , ASP A:130 , GLU A:219 , ASP A:220 , ASN A:222 , HOH A:513 , HOH A:558BINDING SITE FOR RESIDUE NA A 385
3AC3SOFTWARE1PE A:391BINDING SITE FOR RESIDUE NA A 386
4AC4SOFTWAREGLY A:217 , THR A:305 , ARG A:306 , HOH A:452 , HOH A:593BINDING SITE FOR RESIDUE NA A 387
5AC5SOFTWARELYS A:270 , PRO A:300 , LEU A:302 , THR A:305 , HOH A:495BINDING SITE FOR RESIDUE CL A 388
6AC6SOFTWAREARG A:269BINDING SITE FOR RESIDUE CL A 389
7AC7SOFTWARELYS A:52 , GLY A:350BINDING SITE FOR RESIDUE CL A 390
8AC8SOFTWAREASP A:265 , TYR A:283 , MSE A:284 , GLU A:286 , NA A:386BINDING SITE FOR RESIDUE 1PE A 391

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H7K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H7K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H7K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H7K)

(-) Exons   (0, 0)

(no "Exon" information available for 3H7K)

(-) 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:367
 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 d3h7ka_ A: automated matches                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3h7kA00 A:1-376 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.........eeeeee.........hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh....eeee......hhhhhh.eeee..---------..eeeeeee....hhhhhh......hhhhhhhhhhhhhh..eeeeeee.hhh.eee....eeeeehhhhh........hhhhhhhhhhhhhh..eeeee............hhhh.eeeee..eeeeee.....hhhhhhhhhhhhhhh..........eeeeee.......hhhhhhh.......................eee..eeeee.....hhhhhhhhhhhhhh...eeeee..hhhhhh....hhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h7k A   1 SEESRESPAEHGYYmPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEmSmNDSWFRDSGPTFIVRK---------RNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSmILEGGSIHVDGEGTCLVTEECLLNKNRNPHmSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNmCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYmTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHcITQQQPAEPT 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           103       113                                           159-MSE                        190-MSE                               228-MSE                                                 284-MSE                                                                           366-AGT      
                                                                                                                 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 3H7K)

(-) Gene Ontology  (6, 6)

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

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 Related Entries

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        AGUA_ARATH | Q8GWW7: 1vkp 2q3u 3h7c

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