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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BIOSYNTHETIC ARGININE DECARBOXYLASE SPEA FROM CAMPYLOBACTER JEJUNI, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BR53
 
Authors :  F. Forouhar, S. Lew, J. Seetharaman, S. Sahdev, R. Xiao, C. Ciccosanti, R. L. Belote, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelio J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (N
Date :  16 Jul 10  (Deposition) - 01 Sep 10  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Alpha-Beta Protein, Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, S. Lew, J. Seetharaman, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong
Structures Of Bacterial Biosynthetic Arginine Decarboxylases.
Acta Crystallogr. , Sect. F V. 66 1562 2010
PubMed-ID: 21139196  |  Reference-DOI: 10.1107/S1744309110040649

(-) Compounds

Molecule 1 - ARGININE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 21-23C
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CJ0764C, SPEA
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric Unit (3, 25)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 25)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:84 , LYS A:86 , VAL A:87 , ASN A:132 , HIS A:231 , HIS A:233 , SER A:236 , GLN A:237 , GLY A:273 , GLY A:274 , GLU A:320 , SER A:321 , GLY A:322 , ARG A:323 , TYR A:519 , CYS B:483BINDING SITE FOR RESIDUE PLP A 701
2AC2SOFTWAREASN A:11 , GLU A:278 , ARG A:288 , PHE A:324BINDING SITE FOR RESIDUE SO4 A 702
3AC3SOFTWARECYS A:483 , PRO B:84 , LYS B:86 , ASN B:132 , HIS B:231 , HIS B:233 , SER B:236 , GLY B:273 , GLY B:274 , GLU B:320 , SER B:321 , GLY B:322 , ARG B:323 , TYR B:519BINDING SITE FOR RESIDUE PLP B 701
4AC4SOFTWAREGLU A:546 , HIS B:616 , HIS B:617BINDING SITE FOR RESIDUE SO4 B 702
5AC5SOFTWAREARG B:39 , LYS B:44 , GLY B:45 , PRO B:335 , ASN B:443 , LEU B:606 , LYS B:607BINDING SITE FOR RESIDUE SO4 B 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NZP)

(-) 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:583
 aligned with Q0PAC6_CAMJE | Q0PAC6 from UniProtKB/TrEMBL  Length:611

    Alignment length:609
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600         
         Q0PAC6_CAMJE     1 MMDYGIDIWGNENFIIKNGKVCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVGIWAKSGGINSKFGLTSTELIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEYSQFKNEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPSNALEYLHDSIDHLESILTLFDLGYVDLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGLEQNFPIMPLDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGMKHNLFTHPTEAIISINEKGYEVEGIIEAQSILDTLEDLDYDIHAIMDILNERISNSKLVNDKQKKHILGELYLFLNDNGYLKSI 609
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eee....eee......hhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh.hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.......eeeee......-------------....hhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhhhhh......eeeee..................hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhh..eeeeeeeeeee....hhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.-------------....eeee.......hhhhhhh.....eee..............ee.............................eeee....................eeeeeee....eeeeeee...hhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzp A   1 mmDYGIDIWGNENFIIKNGKVCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAmAYNNEGAPITVNGFKDRELINIGFIAAEmGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSA-------------KFGLTSTELIEAVNLLKENKLLEQFTmIHFHLGSQITEIHPLKKALNEAGNIYTELRKmGAKNLKAINLGGGLAVEYSQFKNEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPSNALEYLHDSIDHLESILTLFDLGYVDLQDRSNAEILTHLITKKAILLLG-------------EVQERYLVNFSLFQSmPDFWGLEQNFPImPLDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGmKHNLFTHPTEAIISINEKGYEVEGIIEAQSILDTLEDLDYDIHAImDILNERISNSKLVNDKQKKHILGELYLFLNDNGYLKSI 609
                            ||      10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-         -  |    210       220       230       240       250       260|      270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420|        -    |  440       450       460  |    470       480       490       500       510       520    |  530       540       550       560       570|      580       590       600         
                            ||                                                                                                                   120-MSE                      149-MSE                                 189           203                       229-MSE                         261-MSE                                                                                                                                                         421           435            450-MSE      463-MSE                                                       525-MSE                                       571-MSE                                  
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                             2-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:591
 aligned with Q0PAC6_CAMJE | Q0PAC6 from UniProtKB/TrEMBL  Length:611

    Alignment length:619
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            611        
                                    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       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610|        
         Q0PAC6_CAMJE     1 MMDYGIDIWGNENFIIKNGKVCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINIGFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVGIWAKSGGINSKFGLTSTELIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKMGAKNLKAINLGGGLAVEYSQFKNEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPSNALEYLHDSIDHLESILTLFDLGYVDLQDRSNAEILTHLITKKAILLLGDKQNPADLLAIQDEVQERYLVNFSLFQSMPDFWGLEQNFPIMPLDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGMKHNLFTHPTEAIISINEKGYEVEGIIEAQSILDTLEDLDYDIHAIMDILNERISNSKLVNDKQKKHILGELYLFLNDNGYLKSIGV--------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------Orn_Arg_deC_N-3nzpB01 B:57-328                                                                                                                                                                                                                                                  ---------------------------------------------------------------------------------------------              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------Orn_Arg_deC_N-3nzpB02 B:57-328                                                                                                                                                                                                                                                  ---------------------------------------------------------------------------------------------              ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------              -----------------------------------------------------------------------------------------------------------------------Orn_DAP_Arg_deC-3nzpB03 B:322-538                                                                                                                                                                                        --------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------              -----------------------------------------------------------------------------------------------------------------------Orn_DAP_Arg_deC-3nzpB04 B:322-538                                                                                                                                                                                        --------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .........hhh.eee....eee......hhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh.hhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh.......eeeee.....--------------....hhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhhhhh......eeeee..................hhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhh..eeeeeeeeeeee...hhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh--------------..eeeee.......hhhhhhh.....eee..............ee.............................eeee....................eeeeeee....eeeeeee...hhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzp B   1 mmDYGIDIWGNENFIIKNGKVCINYEKKPAIIDIVKELRDDGYKGPLLLRFPHLIQKQIENIYGNFNKARKEFGYKGGFNAVYPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAmAYNNEGAPITVNGFKDRELINIGFIAAEmGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHS--------------KFGLTSTELIEAVNLLKENKLLEQFTmIHFHLGSQITEIHPLKKALNEAGNIYTELRKmGAKNLKAINLGGGLAVEYSQFKNEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIESGRFVAANHAVLIAPVLELFSQEYAENKLILKKQNPKLIDELYDLYKSIKPSNALEYLHDSIDHLESILTLFDLGYVDLQDRSNAEILTHLITKKAILLLG--------------VQERYLVNFSLFQSmPDFWGLEQNFPImPLDRLDEEPTRSASIWDITCDSDGEISYSKDKPLFLHDVDVEKENYFLGFFLVGAYQEVLGmKHNLFTHPTEAIISINEKGYEVEGIIEAQSILDTLEDLDYDIHAImDILNERISNSKLVNDKQKKHILGELYLFLNDNGYLKSIGVLEHHHHHH 619
                            ||      10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       | -         -  |    210       220       230       240       250       260|      270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420|        -     | 440       450       460  |    470       480       490       500       510       520    |  530       540       550       560       570|      580       590       600       610         
                            1-MSE                                                                                                                120-MSE                      149-MSE                                188            203                       229-MSE                         261-MSE                                                                                                                                                         421            436           450-MSE      463-MSE                                                       525-MSE                                       571-MSE                                            
                             2-MSE
   Legend:   → Mismatch (orange background)
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    → 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 3NZP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NZP)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)
(-)
Clan: no clan defined [family: Orn_DAP_Arg_deC] (18)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q0PAC6_CAMJE | Q0PAC6)
molecular function
    GO:0008792    arginine decarboxylase activity    Catalysis of the reaction: L-arginine + H(+) = agmatine + CO(2).
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0006527    arginine catabolic process    The chemical reactions and pathways resulting in the breakdown of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0008295    spermidine biosynthetic process    The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.

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 Related Entries

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(-) Related Entries Specified in the PDB File

br53