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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PUTATIVE ARGININE DEIMINASE FROM PORPHYROMONAS GINGIVALIS, NORTHEAST STRUCTURAL GENOMICS TARGET PGR3
 
Authors :  F. Forouhar, Y. Chen, A. Kuzin, K. Conover, T. B. Acton, G. T. Montelione J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (N
Date :  08 Apr 05  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Protein. , Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, Y. Chen, A. Kuzin, K. Conover, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Putative Arginine Deiminase From Porphyromonas Gingivalis, Northeast Structural Genomics Target Pgr3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PET21
    Gene: LOCUS_TAG="PG0144"
    Organism Scientific: PORPHYROMONAS GINGIVALIS
    Organism Taxid: 242619
    Strain: W83
    Synonym: AAQ65385

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1ZBR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZBR)

(-) 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:339
 aligned with Q7MXM8_PORGI | Q7MXM8 from UniProtKB/TrEMBL  Length:341

    Alignment length:339
                                    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         
         Q7MXM8_PORGI     3 KRLFLPEWAPQEAVQLTWPHDRTDWAYMLDEVETCFVRIATAILRHERLIVVCPDRKRVFGLLPPELHHRLYCFELPSNDTWARDHGGISLLADGRPMIADFAFNGWGMKFAAHHDNLITRRLHALGLFAEGVTLDNRLAFVLEGGALETDGEGTLLTTDSCLFEPNRNAGLSRTAIIDTLKESLGVSRVLSLRHGALAGDDTDGHIDTLARFVDTRTIVYVRSEDPSDEHYSDLTAMEQELKELRRPDGQPYRLVPLPMAEALYDGADRLPATYANFLIINGAVLVPTYDSHLDAVALSVMQGLFPDREVIGIDCRPLVKQHGSLHCVTMQYPQGFIR 341
               SCOP domains d1zbra1 A:3-341 Putative peptidyl-arginine deiminase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1zbrA00 A:3-341 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh..eeeee......hhhhhh.eeeee..eeeeeeee.hhhhhh....hhhhhhhhhhhh.......eeeeeeeee.hhhhh......eeeeehhhhh........hhhhhhhhhhhhh...eeeee............hhhh.eeeee..eeeeee.......hhhhhhhhhhhhhhh........eeeeee.....ee..ee........eee..eeeeee......hhhhhhhhhhh...eeeeeehhhhhhh..hhhh.eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zbr A   3 KRLFLPEWAPQEAVQLTWPHDRTDWAYmLDEVETCFVRIATAILRHERLIVVCPDRKRVFGLLPPELHHRLYCFELPSNDTWARDHGGISLLADGRPmIADFAFNGWGmKFAAHHDNLITRRLHALGLFAEGVTLDNRLAFVLEGGALETDGEGTLLTTDSCLFEPNRNAGLSRTAIIDTLKESLGVSRVLSLRHGALAGDDTDGHIDTLARFVDTRTIVYVRSEDPSDEHYSDLTAmEQELKELRRPDGQPYRLVPLPmAEALYDGADRLPATYANFLIINGAVLVPTYDSHLDAVALSVmQGLFPDREVIGIDCRPLVKQHGSLHCVTmQYPQGFIR 341
                                    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|        
                                                      30-MSE                                                               100-MSE    111-MSE                                                                                                                          240-MSE               262-MSE                                   304-MSE                      333-MSE    


Chain B from PDB  Type:PROTEIN  Length:339
 aligned with Q7MXM8_PORGI | Q7MXM8 from UniProtKB/TrEMBL  Length:341

    Alignment length:339
                                    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         
         Q7MXM8_PORGI     3 KRLFLPEWAPQEAVQLTWPHDRTDWAYMLDEVETCFVRIATAILRHERLIVVCPDRKRVFGLLPPELHHRLYCFELPSNDTWARDHGGISLLADGRPMIADFAFNGWGMKFAAHHDNLITRRLHALGLFAEGVTLDNRLAFVLEGGALETDGEGTLLTTDSCLFEPNRNAGLSRTAIIDTLKESLGVSRVLSLRHGALAGDDTDGHIDTLARFVDTRTIVYVRSEDPSDEHYSDLTAMEQELKELRRPDGQPYRLVPLPMAEALYDGADRLPATYANFLIINGAVLVPTYDSHLDAVALSVMQGLFPDREVIGIDCRPLVKQHGSLHCVTMQYPQGFIR 341
               SCOP domains d1zbrb_ B: automated matches                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1zbrB00 B:3-341 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) -PAD_porph-1zbrB01 B:4-336                                                                                                                                                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) -PAD_porph-1zbrB02 B:4-336                                                                                                                                                                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author .eee......eeeeeee............hhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh...hhh.eeeee......hhhhhh.eeeee..eeeeeeee.hhhhhh....hhhhhhhhhhhh.......eeeeeeeee.hhhhh......eeeeehhhhh........hhhhhhhhhhhhh...eeeee............hhhh.eeeee..eeeeee.......hhhhhhhhhhhhhhh........eeeeee...................eee..eeeeee....hhhhhhhhhhhhh...eeeeeehhhhhh...hhhh.eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zbr B   3 KRLFLPEWAPQEAVQLTWPHDRTDWAYmLDEVETCFVRIATAILRHERLIVVCPDRKRVFGLLPPELHHRLYCFELPSNDTWARDHGGISLLADGRPmIADFAFNGWGmKFAAHHDNLITRRLHALGLFAEGVTLDNRLAFVLEGGALETDGEGTLLTTDSCLFEPNRNAGLSRTAIIDTLKESLGVSRVLSLRHGALAGDDTDGHIDTLARFVDTRTIVYVRSEDPSDEHYSDLTAmEQELKELRRPDGQPYRLVPLPmAEALYDGADRLPATYANFLIINGAVLVPTYDSHLDAVALSVmQGLFPDREVIGIDCRPLVKQHGSLHCVTmQYPQGFIR 341
                                    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|        
                                                      30-MSE                                                               100-MSE    111-MSE                                                                                                                          240-MSE               262-MSE                                   304-MSE                      333-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  (2, 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  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7MXM8_PORGI | Q7MXM8)
molecular function
    GO:0004668    protein-arginine deiminase activity    Catalysis of the reaction: protein L-arginine + H2O = protein L-citrulline + NH3.
biological process
    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.

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(-) Related Entries Specified in the PDB File

pgr3