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(-) Description

Title :  ORNITHINE DECARBOXYLASE MUTANT (GLY121TYR)
 
Authors :  J. Vitali, M. L. Hackert
Date :  26 Aug 99  (Deposition) - 26 Feb 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Keywords :  Decarboxylase, Ornithine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Vitali, D. Carroll, R. G. Chaudhry, M. L. Hackert
Three-Dimensional Structure Of The Gly121Tyr Dimeric Form O Ornithine Decarboxylase From Lactobacillus 30A.
Acta Crystallogr. , Sect. D V. 55 1978 1999
PubMed-ID: 10666573  |  Reference-DOI: 10.1107/S0907444999010756

(-) Compounds

Molecule 1 - PROTEIN (ORNITHINE DECARBOXYLASE)
    Chains: A
    EC Number: 4.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: L30A ODC
    Expression System Plasmid: PET21A
    Expression System Strain: HMS174/DE3
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: LACTOBACILLUS SP. 30A
    Organism Taxid: 1593
    Strain: 30A

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:197 , SER A:198 , SER A:199 , ASN A:202 , HIS A:223 , GLN A:288 , ASP A:316 , ALA A:318 , SER A:352 , HIS A:354 , LYS A:355 , SER A:394 , THR A:395 , SER A:396BINDING SITE FOR RESIDUE PLP A 955
2AC2SOFTWAREHIS A:171 , GLU A:179 , LYS A:180 , LYS A:190 , THR A:191 , TYR A:192 , LYS A:374 , TYR A:379 , ASP A:381 , HIS A:382 , LYS A:383 , HOH A:1165 , HOH A:1170BINDING SITE FOR RESIDUE GTP A 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C4K)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Cys A:127 -Pro A:128
2Tyr A:660 -Pro A:661
3Pro A:661 -Pro A:662

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C4K)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OKR_DC_1PS00703 Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.DCOR_LACS3351-365  1A:350-364
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OKR_DC_1PS00703 Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.DCOR_LACS3351-365  2A:350-364
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OKR_DC_1PS00703 Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.DCOR_LACS3351-365  2A:350-364

(-) Exons   (0, 0)

(no "Exon" information available for 1C4K)

(-) 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:728
 aligned with DCOR_LACS3 | P43099 from UniProtKB/Swiss-Prot  Length:731

    Alignment length:730
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731
           DCOR_LACS3     2 SSSLKIASTQEARQYFDTDRVVVDAVGSDFTDVGAVIAMDYETDVIDAADATKFGIPVFAVTKDAQAISADELKKIFHIIDLENKFDATVNAREIETAVNNYEDSILPPFFKSLKEYVSRGLIQFDCPGHQGGQYYRKHPAGREFYDFFGETVFRADLCNADVALGDLLIHEGPAVAAEKHAARVYNADKTYFVLGGSSNANNTVTSALVSNGDLVLFDRNNHKSVYNSALAMAGGRPVYLQTNRNPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHFNNSFNLFMSTSPFYPMYAALDVNAAMQEGEAGRKLWHDLLITTIEARKKLIKAGSMFRPFVPPVVNGKKWEDGDTEDMANNIDYWRFEKGAKWHAYEGYGDNQYYVDPNKFMLTTPGINPETGDYEDFGVPATIVANYLRDHGIIPEKSDLNSILFLMTPAETPAKMNNLITQLLQLQRLIEEDAPLKQVLPSIYAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNHNKLVPLNKIEGEIALEGALPYPPGVFCVAPGEKWSETAVKYFTILQDGINNFPGFAPEIQGVYFKQEGDKVVAYGEVYDAEVAKNDDRYNN 731
               SCOP domains d1c4ka1 A:1-107 Ornithine decarboxylase N-terminal wing domain                                             d1c4ka2 A:108-569 Ornithine decarboxylase major domain                                                                                                                                                                                                                                                                                                                                                                                                                        d1c4ka3 A:570-730 Ornithine decarboxylase C-terminal domain                                                                                                       SCOP domains
               CATH domains 1c4kA01 A:1-107  [code=3.40.50.220, no name defined]                                                       1c4kA02 A:108-420 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                                                    1c4kA03 A:421-600 Aspartate Aminotransferase, domain 1                                                                                                                              1c4kA04 A:601-729 Ornithine Decarboxylase, subunit A, domain 4                                                                   - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhh.......eee.........eeeee....hhhhhhhhhh....eeeeee.......hhhhhh..eee...--..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.............hhhhh..hhhhhhhhhh.hhhhhh.................hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh....eeeeee....hhhhhhhhh....eeeee...................hhhhhhhh...hhhh.......eeeee...........hhhhhhhh.....eeeeee....hhhh....................eeeeeee...........eeeeee............hhhhhhhhhhh......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....eee..............hhhhhh............................eeeeeee.................hhhhhhhhh.....eeee..eeeeee.....hhhhhhhhhhhhhhhhhhh.........hhhhhhh........hhhhhhhhhhhhhhh..hhhhhhh...........hhhhhhhhhhh.eeeee........eee..ee.......ee...ee.hhhhhhhhhhhhhhhh.......eee..eeeee..eeeee.eeeehhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------OKR_DC_1       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c4k A   1 SSSLKIASTQEARQYFDTDRVVVDAVGSDFTDVGAVIAMDYETDVIDAADATKFGIPVFAVTKDAQAISADELKKIFHIIDLE--FDATVNAREIETAVNNYEDSILPPFFKSLKEYVSRYLIQFDCPGHQGGQYYRKHPAGREFYDFFGETVFRADLCNADVALGDLLIHEGPAVAAEKHAARVYNADKTYFVLGGSSNANNTVTSALVSNGDLVLFDRNNHKSVYNSALAMAGGRPVYLQTNRNPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHFNNSFNLFMSTSPFYPMYAALDVNAAMQEGEAGRKLWHDLLITTIEARKKLIKAGSMFRPFVPPVVNGKKWEDGDTEDMANNIDYWRFEKGAKWHAYEGYGDNQYYVDPNKFMLTTPGINPETGDYEDFGVPATIVANYLRDHGIIPEKSDLNSILFLMTPAETPAKMNNLITQLLQLQRLIEEDAPLKQVLPSIYAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNHNKLVPLNKIEGEIALEGALPYPPGVFCVAPGEKWSETAVKYFTILQDGINNFPGFAPEIQGVYFKQEGDKVVAYGEVYDAEVAKNDDRYNN 730
                                    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       620       630       640       650       660       670       680       690       700       710       720       730
                                                                                                             83 86
   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  (3, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C4K)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCOR_LACS3 | P43099)
molecular function
    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:0004586    ornithine decarboxylase activity    Catalysis of the reaction: L-ornithine + H(+) = CO(2) + putrescine.
biological process
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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