1D7K - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE AT 2.1 ANGSTROMS RESOLUTION

Authors :   J. J. Almrud, M. A. Oliveira, A. D. Kern, N. V. Grishin, M. A. Phillips, M. L. Hackert

Date :   18 Oct 99 (Deposition) - 25 Oct 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Alpha-Beta Barrel, Pyridoxal 5'-Phosphate, Sheet-Domain, Decarboxylation, Ornithine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Almrud, M. A. Oliveira, A. D. Kern, N. V. Grishin, M. A. Phillips, M. L. Hackert
Crystal Structure Of Human Ornithine Decarboxylase At 2. 1 A Resolution: Structural Insights To Antizyme Binding.
J. Mol. Biol. V. 295 7 2000
PubMed-ID: 10623504 | Reference-DOI: 10.1006/JMBI.1999.3331
(for further references see the PDB file header)

Molecule 1 - HUMAN ORNITHINE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET WITH N-TERMINAL (HIS)6 TAG
	Organ	:	LIVER
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

(no "Site" information available for 1D7K)

(no "SS Bond" information available for 1D7K)

(no "Cis Peptide Bond" information available for 1D7K)

(no "SAP(SNP)/Variant" information available for 1D7K)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ODR_DC_2_1	PS00878	Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.	DCOR_HUMAN	66-84	2	A:66-84 B:66-84
2	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	DCOR_HUMAN	222-239	2	A:222-239 B:222-239

Asymmetric/Biological Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000234111	1a	ENSE00001349715	chr2:10588630-10588247	384	DCOR_HUMAN	-	0	0	-	-
1.3	ENST00000234111	3	ENSE00001349711	chr2:10585390-10585281	110	DCOR_HUMAN	-	0	0	-	-
1.4	ENST00000234111	4	ENSE00002192373	chr2:10585175-10585057	119	DCOR_HUMAN	1-34	34	2	A:7-34 B:7-34	28 28
1.5b	ENST00000234111	5b	ENSE00000710607	chr2:10584773-10584600	174	DCOR_HUMAN	35-92	58	2	A:35-92 B:35-92	58 58
1.6	ENST00000234111	6	ENSE00001687557	chr2:10584393-10584221	173	DCOR_HUMAN	93-150	58	2	A:93-150 B:93-150	58 58
1.7	ENST00000234111	7	ENSE00000710605	chr2:10583962-10583828	135	DCOR_HUMAN	150-195	46	2	A:150-195 B:150-195	46 46
1.8	ENST00000234111	8	ENSE00000710603	chr2:10583697-10583616	82	DCOR_HUMAN	195-222	28	2	A:195-222 B:195-222	28 28
1.9	ENST00000234111	9	ENSE00000710602	chr2:10583439-10583356	84	DCOR_HUMAN	223-250	28	2	A:223-250 B:223-250	28 28
1.10	ENST00000234111	10	ENSE00000710601	chr2:10582300-10582138	163	DCOR_HUMAN	251-305	55	2	A:251-301 B:251-300	51 50
1.11	ENST00000234111	11	ENSE00000710600	chr2:10582055-10581943	113	DCOR_HUMAN	305-342	38	2	A:311-342 B:309-342	32 34
1.12	ENST00000234111	12	ENSE00000710599	chr2:10581849-10581635	215	DCOR_HUMAN	343-414	72	2	A:343-414 B:343-414	72 72
1.13b	ENST00000234111	13b	ENSE00001001268	chr2:10580994-10580094	901	DCOR_HUMAN	414-461	48	2	A:414-427 B:414-421	14 8

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
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Chain A from PDB  Type:PROTEIN  Length:412
 aligned with DCOR_HUMAN | P11926 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:421
                                    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       386       396       406       416       426 
           DCOR_HUMAN     7 EEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDEKYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQFQNPDFPP 427
               SCOP domains d1d7ka1 A:7-43,A:284-427             d1d7ka2 A:44-283 Eukaryotic ornithine decarboxylase                                                                                                                                                                                             d1d7ka1 A:7-43,A:2         84-427 Eukaryotic ornithine decarboxylase (ODC)                                                                       SCOP domains
               CATH domains ----------------------------1d7kA01    1d7kA02 A:46-279 Alanine racemase                                                                                                                                                                                                         1d7kA01 A:35-45,A:280-         409 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                              ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....hhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh.eeee.hhhhhhhhhh...hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeee..................hhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh..eeeeeeeeeeeee.....---------..eeeeee.......hhhhhhh......ee.........eeeeeee........eeeeeeeee......eeee......hhhhh.hhhhh...eeeeeehhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------ODR_DC_2_1         -----------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:7-34       Exon 1.5b  PDB: A:35-92 UniProt: 35-92                    Exon 1.6  PDB: A:93-150 UniProt: 93-150                   --------------------------------------------Exon 1.8  PDB: A:195-222    Exon 1.9  PDB: A:223-250    Exon 1.10  PDB: A:251-301 UniProt: 251-305 [INCOMPLETE]-------------------------------------Exon 1.12  PDB: A:343-414 UniProt: 343-414                              ------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:150-195 UniProt: 150-195     -------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: A:311-342 [INCOMPLETE]-----------------------------------------------------------------------Exon 1.13b     Transcript 1 (2)
                 1d7k A   7 EEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVkCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQT---------EQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDERYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQFQNPDFPP 427
                                    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    |    -    |  316       326       336       346       356       366       376       386       396       406       416       426 
                                                                                         69-LLP                                                                                                                                                                                                                                 301       311

Chain B from PDB  Type:PROTEIN  Length:407
 aligned with DCOR_HUMAN | P11926 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:415
                                    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       386       396       406       416     
           DCOR_HUMAN     7 EEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDEKYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQFQ 421
               SCOP domains d1d7kb1 B:7-43,B:284-421             d1d7kb2 B:44-283 Eukaryotic ornithine decarboxylase                                                                                                                                                                                             d1d7kb1 B:7-43,B:        284-421 Eukaryotic ornithine decarboxylase (ODC)                                                                  SCOP domains
               CATH domains ----------------------------1d7kB01    1d7kB02 B:46-279 Alanine racemase                                                                                                                                                                                                         1d7kB01 B:35-45,B:280        -409 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                               ------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....hhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhh...eeee.hhhhhhhhhh...hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeee..................hhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhhh......eee.............hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh..eeeeeeeeeeeee....--------....eeeeee.....hhhhhhhhh......ee.........eeeeeee........eeeeeeeee......eeee......hhhhh.hhhhh...eeeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------ODR_DC_2_1         -----------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: B:7-34       Exon 1.5b  PDB: B:35-92 UniProt: 35-92                    Exon 1.6  PDB: B:93-150 UniProt: 93-150                   --------------------------------------------Exon 1.8  PDB: B:195-222    Exon 1.9  PDB: B:223-250    Exon 1.10  PDB: B:251-300 UniProt: 251-305 [INCOMPLETE]-------------------------------------Exon 1.12  PDB: B:343-414 UniProt: 343-414                              ------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: B:150-195 UniProt: 150-195     -------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: B:309-342 [INCOMPLETE]-----------------------------------------------------------------------1.13b    Transcript 1 (2)
                 1d7k B   7 EEFDCHFLDEGFTAKDILDQKINEVSSSDDKDAFYVADLGDILKKHLRWLKALPRVTPFYAVkCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQ--------SSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPKPDERYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIYYVMSGPAWQLMQQFQ 421
                                    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   |     -  |    316       326       336       346       356       366       376       386       396       406       416     
                                                                                         69-LLP                                                                                                                                                                                                                                300      309

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Alanine racemase (53)

Human (Homo sapiens) (3)

1a	1d7kA02	A:46-279
1b	1d7kB02	B:46-279

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Homologous Superfamily: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Human (Homo sapiens) (3)

2a	1d7kB01	B:35-45,B:280-409
2b	1d7kA01	A:35-45,A:280-409

(no "Pfam Domain" information available for 1D7K)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DCOR_HUMAN | P11926)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0001822	kidney development	The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
	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:0006595	polyamine metabolic process	The chemical reactions and pathways involving polyamines, any organic compound containing two or more amino groups.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	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:0033387	putrescine biosynthetic process from ornithine	The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane by decarboxylation of ornithine.
	GO:0006521	regulation of cellular amino acid metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids.
	GO:0042176	regulation of protein catabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0009615	response to virus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric/Biological Unit
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