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(-) Description

Title :  CRYSTAL STRUCTURE OF L-TYROSINE DECARBOXYLASE MFNA (EC 4.1.1.25) (NP_247014.1) FROM METHANOCOCCUS JANNASCHII AT 2.11 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  14 Nov 08  (Deposition) - 25 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_247014. 1, L-Tyrosine Decarboxylase Mfna (Ec 4. 1. 1. 25), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Decarboxylase, Lyase, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of L-Tyrosine Decarboxylase Mfna (Ec 4. 1. 1. 25) (Np_247014. 1) From Methanococcus Jannaschii At 2. 11 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-TYROSINE DECARBOXYLASE MFNA
    Chains: A, B
    EC Number: 4.1.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Vector Type: PLASMID
    Gene: MFNA, MJ0050, NP_247014.1
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: TDC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric/Biological Unit (3, 22)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE17Mod. Amino AcidSELENOMETHIONINE
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:37 , GLY A:93 , GLY A:94 , THR A:95 , ASN A:98 , HIS A:132 , THR A:181 , ASP A:206 , ALA A:208 , ASP A:242 , HIS A:244 , LYS A:245 , HOH A:580 , HOH A:587 , HOH A:700 , THR B:285BINDING SITE FOR RESIDUE PLP A 500
2AC2SOFTWARETHR A:285 , MSE B:37 , GLY B:93 , GLY B:94 , THR B:95 , ASN B:98 , HIS B:132 , THR B:181 , ASP B:206 , ALA B:208 , ASP B:242 , HIS B:244 , LYS B:245 , HOH B:482 , HOH B:506 , HOH B:719BINDING SITE FOR RESIDUE PLP B 500
3AC3SOFTWAREPRO A:272 , HOH A:512 , ALA B:131 , HIS B:132 , HOH B:519BINDING SITE FOR RESIDUE MPD B 397
4AC4SOFTWAREILE A:129 , ALA A:131 , HOH A:539 , HOH B:714BINDING SITE FOR RESIDUE MPD A 397
5AC5SOFTWAREASP A:50BINDING SITE FOR RESIDUE MPD A 398

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F9T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:251 -Pro A:252
2Ile B:251 -Pro B:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3F9T)

(-) Exons   (0, 0)

(no "Exon" information available for 3F9T)

(-) 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:394
 aligned with MFNA_METJA | Q60358 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:394
                                    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    
           MFNA_METJA     1 MRNMQEKGVSEKEILEELKKYRSLDLKYEDGNIFGSMCSNVLPITRKIVDIFLETNLGDPGLFKGTKLLEEKAVALLGSLLNNKDAYGHIVSGGTEANLMALRCIKNIWREKRRKGLSKNEHPKIIVPITAHFSFEKGREMMDLEYIYAPIKEDYTIDEKFVKDAVEDYDVDGIIGIAGTTELGTIDNIEELSKIAKENNIYIHVDAAFGGLVIPFLDDKYKKKGVNYKFDFSLGVDSITIDPHKMGHCPIPSGGILFKDIGYKRYLDVDAPYLTETRQATILGTRVGFGGACTYAVLRYLGREGQRKIVNECMENTLYLYKKLKENNFKPVIEPILNIVAIEDEDYKEVCKKLRDRGIYVSVCNCVKALRIVVMPHIKREHIDNFIEILNSIK 394
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh...hhhhh...........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhh.eeeee........hhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhh........hhhhh..eee.............eeeee.hhhhhhhh.ee.......ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee..hhhhhhhhhhhh....ee.....eeeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f9t A   1 mRNmQEKGVSEKEILEELKKYRSLDLKYEDGNIFGSmCSNVLPITRKIVDIFLETNLGDPGLFKGTKLLEEKAVALLGSLLNNKDAYGHIVSGGTEANLmALRCIKNIWREKRRKGLSKNEHPKIIVPITAHFSFEKGREmmDLEYIYAPIKEDYTIDEKFVKDAVEDYDVDGIIGIAGTTELGTIDNIEELSKIAKENNIYIHVDAAFGGLVIPFLDDKYKKKGVNYKFDFSLGVDSITIDPHKmGHCPIPSGGILFKDIGYKRYLDVDAPYLTETRQATILGTRVGFGGACTYAVLRYLGREGQRKIVNECmENTLYLYKKLKENNFKPVIEPILNIVAIEDEDYKEVCKKLRDRGIYVSVCNCVKALRIVVmPHIKREHIDNFIEILNSIK 394
                            |  |    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    
                            |  |                               37-MSE                                                        100-MSE                                  141-MSE                                                                                                  246-MSE                                                             314-MSE                                                      375-MSE               
                            1-MSE                                                                                                                                      142-MSE                                                                                                                                                                                                                                                        
                               4-MSE                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:392
 aligned with MFNA_METJA | Q60358 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:392
                                    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       342       352       362       372       382       392  
           MFNA_METJA     3 NMQEKGVSEKEILEELKKYRSLDLKYEDGNIFGSMCSNVLPITRKIVDIFLETNLGDPGLFKGTKLLEEKAVALLGSLLNNKDAYGHIVSGGTEANLMALRCIKNIWREKRRKGLSKNEHPKIIVPITAHFSFEKGREMMDLEYIYAPIKEDYTIDEKFVKDAVEDYDVDGIIGIAGTTELGTIDNIEELSKIAKENNIYIHVDAAFGGLVIPFLDDKYKKKGVNYKFDFSLGVDSITIDPHKMGHCPIPSGGILFKDIGYKRYLDVDAPYLTETRQATILGTRVGFGGACTYAVLRYLGREGQRKIVNECMENTLYLYKKLKENNFKPVIEPILNIVAIEDEDYKEVCKKLRDRGIYVSVCNCVKALRIVVMPHIKREHIDNFIEILNSIK 394
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh...hhhhh...........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhh.eeeee........hhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhh........hhhhh..eee.............eeeee.hhhhhhhh.ee.......ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeee..hhhhhhhhhhhh....ee.....eeeee.....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f9t B   3 NmQEKGVSEKEILEELKKYRSLDLKYEDGNIFGSmCSNVLPITRKIVDIFLETNLGDPGLFKGTKLLEEKAVALLGSLLNNKDAYGHIVSGGTEANLmALRCIKNIWREKRRKGLSKNEHPKIIVPITAHFSFEKGREmmDLEYIYAPIKEDYTIDEKFVKDAVEDYDVDGIIGIAGTTELGTIDNIEELSKIAKENNIYIHVDAAFGGLVIPFLDDKYKKKGVNYKFDFSLGVDSITIDPHKmGHCPIPSGGILFKDIGYKRYLDVDAPYLTETRQATILGTRVGFGGACTYAVLRYLGREGQRKIVNECmENTLYLYKKLKENNFKPVIEPILNIVAIEDEDYKEVCKKLRDRGIYVSVCNCVKALRIVVmPHIKREHIDNFIEILNSIK 394
                             |      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       342       352       362       372  |    382       392  
                             4-MSE                           37-MSE                                                        100-MSE                                  141-MSE                                                                                                  246-MSE                                                             314-MSE                                                      375-MSE               
                                                                                                                                                                     142-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  (0, 0)

(no "SCOP Domain" information available for 3F9T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F9T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F9T)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MFNA_METJA | Q60358)
molecular function
    GO:0004068    aspartate 1-decarboxylase activity    Catalysis of the reaction: L-aspartate = beta-alanine + CO2.
    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.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0004837    tyrosine decarboxylase activity    Catalysis of the reaction: L-tyrosine = tyramine + CO2.
biological process
    GO:0019752    carboxylic acid metabolic process    The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
    GO:2001120    methanofuran biosynthetic process    The chemical reactions and pathways resulting in the formation of a methanofuran.

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  MFNA_METJA | Q60358
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