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(-) Description

Title :  X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G08170, AGMATINE IMINOHYDROLASE
 
Authors :  G. E. Wesenberg, D. W. Smith, G. N. Phillips Jr. , C. A. Bingman, S. T. M. Allard, Center For Eukaryotic Structural Genomics (Cesg)
Date :  15 Jun 04  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, At5G08170, Polyamine Biosynthesis, Agmatine Iminohydrolase, Aih, Agmatine Deiminase, N-Carbamoylputrescine, Putrescine, Psi, Center For Eukaryotic Structural Genomics, Cesg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Center For Eukaryotic Structural Genomics
X-Ray Structure Of Gene Product From Arabidopsis Thaliana At5G08170
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AGMATINE IMINOHYDROLASE
    Chains: A, B
    EC Number: 3.5.3.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AT5G08170
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: AIH, AGMATINE DEIMINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 30)

Asymmetric/Biological Unit (4, 30)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL
2MG2Ligand/IonMAGNESIUM ION
3MPO1Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
4MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:119 , TRP A:120 , SER A:143 , HOH A:1040 , HOH A:1056 , HOH A:1181BINDING SITE FOR RESIDUE MG A 802
02AC2SOFTWAREASP B:119 , TRP B:120 , SER B:143 , HOH B:929 , HOH B:944 , HOH B:986BINDING SITE FOR RESIDUE MG B 801
03AC3SOFTWAREASN A:35 , TRP A:91 , THR A:221 , ARG A:301 , ALA A:360 , EDO A:903 , HOH A:1228BINDING SITE FOR RESIDUE EDO A 901
04AC4SOFTWAREARG A:337 , VAL A:338 , HOH A:1079BINDING SITE FOR RESIDUE EDO A 902
05AC5SOFTWARETRP A:91 , ASP A:94 , TRP A:125 , GLY A:361 , CYS A:366 , EDO A:901BINDING SITE FOR RESIDUE EDO A 903
06AC6SOFTWAREASN A:123 , LYS A:184 , ASN A:185 , ARG A:186 , PRO A:188BINDING SITE FOR RESIDUE EDO A 906
07AC7SOFTWARETYR A:216 , GLY A:217 , ASP A:218 , GLU A:219 , ARG A:252 , HOH A:1066BINDING SITE FOR RESIDUE EDO A 907
08AC8SOFTWAREVAL A:83 , GLU A:84 , LEU A:149 , HOH A:1038 , HOH A:1100 , VAL B:83 , GLU B:84 , LEU B:149BINDING SITE FOR RESIDUE EDO A 908
09AC9SOFTWAREASP A:244 , THR A:246BINDING SITE FOR RESIDUE EDO A 910
10BC1SOFTWARETYR A:14 , GLY A:170 , GLU A:171 , GLY A:172 , GLY A:204 , GLN A:206 , HOH A:1229BINDING SITE FOR RESIDUE MPO A 1000
11BC2SOFTWARETRP B:91 , ASP B:94 , THR B:221 , GLY B:361 , GLY B:362 , CYS B:366 , HOH B:981BINDING SITE FOR RESIDUE EDO B 904
12BC3SOFTWARETRP B:19 , ALA B:232 , ARG B:233 , HIS B:346 , HOH B:1274BINDING SITE FOR RESIDUE EDO B 905
13BC4SOFTWARESER B:55 , PHE B:57 , GLU B:58 , PRO B:59 , HOH B:1145BINDING SITE FOR RESIDUE EDO B 909
14BC5SOFTWARETRP B:125 , ASP B:130 , ASN B:185 , GLU B:219 , ASP B:220 , ASN B:222BINDING SITE FOR RESIDUE EDO B 911
15BC6SOFTWARESER B:7 , ARG B:154 , PHE B:155 , GLN B:156 , HOH B:963BINDING SITE FOR RESIDUE EDO B 912
16BC7SOFTWARETYR B:14 , PRO B:16 , ASP B:20 , ALA B:373 , HOH B:970BINDING SITE FOR RESIDUE EDO B 913

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VKP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VKP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VKP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VKP)

(-) Exons   (0, 0)

(no "Exon" information available for 1VKP)

(-) 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:365
 aligned with AGUA_ARATH | Q8GWW7 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:372
                                    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  
           AGUA_ARATH     5 RESPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFADVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRPVKLSSLNRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
               SCOP domains d1vkpa_ A: Agmatine iminohydrolase                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1vkpA00 A:5-376 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.........eeeeee.........hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh....eeee......hhhhhh.eeee...-------...eeeeeee....hhhhhh......hhhhhhhhhhhhhh..eeeeeee.hhh.eee....eeeeehhhhh........hhhhhhhhhhhhhh..eeeee............hhhh.eeeee..eeeeee......hhhhhhhhhhhhhhh.........eeeeee........hh.hhhh......................eee..eeeee...hhhhhhhhhhhhhhhh...eeeee..hhhhhh....hhh.eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vkp A   5 RESPAEHGYYmPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEmSmNDSWFRDSGPTFIVRKR-------NRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSmILEGGSIHVDGEGTCLVTEECLLNKNRNPHmSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNmCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYmTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
                                    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  
                                     15-MSE                                                                85-MSE            104     112                                            159-MSE                        190-MSE                               228-MSE                                                 284-MSE                                                                                        
                                                                                                             87-MSE                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:363
 aligned with AGUA_ARATH | Q8GWW7 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:370
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376
           AGUA_ARATH     7 SPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFADVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRPVKLSSLNRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
               SCOP domains d1vkpb_ B: Agmatine iminohydrolase                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1vkpB00 B:7-376 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ------PAD_porph-1vkpB01 B:13-372                                                                                                                                                                                                                                                                                                                                              ---- Pfam domains (1)
           Pfam domains (2) ------PAD_porph-1vkpB02 B:13-372                                                                                                                                                                                                                                                                                                                                              ---- Pfam domains (2)
         Sec.struct. author hhhhhh.........eeeeee.........hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhh....eeee......hhhhhh.eeee...-------...eeeeeee....hhhhhh......hhhhhhhhhhhhhh..eeeeeee.hhh.eee....eeeeehhhhh........hhhhhhh.hhhhhh..eeeee............hhhh.eeeee..eeeeee......hhhhhhhhhhhhhhh.........eeeeee.......hhhhhhh.......................eee..eeeee...hhhhhhhhhhhhhhhh...eeeee..hhhhhh...hhhhheeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vkp B   7 SPAEHGYYmPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEmSmNDSWFRDSGPTFIVRKR-------NRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSmILEGGSIHVDGEGTCLVTEECLLNKNRNPHmSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNmCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYmTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPT 376
                                    16        26        36        46        56        66        76        86|       96       | -     | 116       126       136       146       156  |    166       176       186   |   196       206       216       226 |     236       246       256       266       276       286       296       306       316       326       336       346       356       366       376
                                   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)
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  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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GME (20)

(-) Gene Ontology  (6, 6)

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

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

UniProtKB/Swiss-Prot
        AGUA_ARATH | Q8GWW7: 2q3u 3h7c 3h7k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VKP)