1ORD - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASE FROM LACTOBACILLUS 30A TO 3.1 ANGSTROMS RESOLUTION

Authors :   M. L. Hackert, C. Momany, S. Ernst, R. Ghosh

Date :   08 Feb 95 (Deposition) - 15 Sep 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (6x)

Keywords :   Carboxy-Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Momany, S. Ernst, R. Ghosh, N. L. Chang, M. L. Hackert
Crystallographic Structure Of A Plp-Dependent Ornithine Decarboxylase From Lactobacillus 30A To 3. 0 A Resolution.
J. Mol. Biol. V. 252 643 1995
PubMed-ID: 7563080 | Reference-DOI: 10.1006/JMBI.1995.0526
(for further references see the PDB file header)

Molecule 1 - ORNITHINE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.17
	Organism Scientific	:	LACTOBACILLUS SP.
	Organism Taxid	:	1593
	Strain	:	30A

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (6x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	PLP	12	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:197 , SER A:198 , SER A:199 , HIS A:223 , SER A:225 , GLN A:288 , ASP A:316 , ALA A:318 , TRP A:319 , SER A:352 , HIS A:354 , LYS A:355 , SER B:394 , THR B:395 , SER B:396	BINDING SITE FOR RESIDUE PLP A 731
2	AC2	SOFTWARE	SER A:394 , THR A:395 , SER A:396 , GLY B:197 , SER B:198 , SER B:199 , HIS B:223 , SER B:225 , GLN B:288 , ASP B:316 , ALA B:318 , TRP B:319 , SER B:352 , HIS B:354 , LYS B:355	BINDING SITE FOR RESIDUE PLP B 731
3	PLA	UNKNOWN	PLP A:731	NULL
4	PLB	UNKNOWN	PLP B:731	NULL

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

Asymmetric Unit

No.	Residues
1	Cys A:127	-	Pro A:128
2	Tyr A:660	-	Pro A:661
3	Pro A:661	-	Pro A:662
4	Cys B:127	-	Pro B:128
5	Tyr B:660	-	Pro B:661
6	Pro B:661	-	Pro B:662

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OKR_DC_1	PS00703	Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.	DCOR_LACS3	351-365	2	A:350-364 B:350-364

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OKR_DC_1	PS00703	Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.	DCOR_LACS3	351-365	2	A:350-364 B:350-364

Biological Unit 2 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OKR_DC_1	PS00703	Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.	DCOR_LACS3	351-365	12	A:350-364 B:350-364

(no "Exon" information available for 1ORD)

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:730
 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 d1orda1 A:1-107 Ornithine decarboxylase N-terminal wing domain                                             d1orda2 A:108-569 Ornithine decarboxylase major domain                                                                                                                                                                                                                                                                                                                                                                                                                        d1orda3 A:570-730 Ornithine decarboxylase C-terminal domain                                                                                                       SCOP domains
               CATH domains 1ordA01 A:1-107  [code=3.40.50.220, no name defined]                                                       1ordA02 A:108-420 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                                                    1ordA03 A:421-600 Aspartate Aminotransferase, domain 1                                                                                                                              1ordA04 A:601-730 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
                 1ord A   1 SSSLKIASTQEARQYFDTDRVVVDAVGSDFTDVGAVIAMDYETDVIDAADATKFGIPVFAVTKDAQAISADELKKIFHIIDLENKFDATVNAREIETAVNNYEDSILPPFFKSLKEYVSRGLIQFDCPGHQGGQYYRKHPAGREFYDFFGETVFRADLCNADVALGDLLIHEGPAVAAEKHAARVYNADKTYFVLGGSSNANNTVTSALVSNGDLVLFDRNNHKSVYNSALAMAGGRPVYLQTNRNPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHFNNSFNLFMSTSPFYPMYAALDVNAAMQEGEAGRKLWHDLLITTIEARKKLIKAGSMFRPFVPPVVNGKKWEDGDTEDMANNIDYWRFEKGAKWHAYEGYGDNQYYVDPNKFMLTTPGINPETGDYEDFGVPATIVANYLRDHGIIPEKSDLNSILFLMTPAETPAKMNNLITQLLQLQRLIEEDAPLKQVLPSIYAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNHNKLVPLNKIEGEIALEGALPYPPGVFCVAPGEKWSETAVKYFTILQDGINNFPGFAPEIQGVYFKQEGDKVVAYGEVYDAEVAKNDDRYNN 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

Chain B from PDB  Type:PROTEIN  Length:730
 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 d1ordb1 B:1-107 Ornithine decarboxylase N-terminal wing domain                                             d1ordb2 B:108-569 Ornithine decarboxylase major domain                                                                                                                                                                                                                                                                                                                                                                                                                        d1ordb3 B:570-730 Ornithine decarboxylase C-terminal domain                                                                                                       SCOP domains
               CATH domains 1ordB01 B:1-107  [code=3.40.50.220, no name defined]                                                       1ordB02 B:108-420 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                                                                    1ordB03 B:421-600 Aspartate Aminotransferase, domain 1                                                                                                                              1ordB04 B:601-730 Ornithine Decarboxylase, subunit A, domain 4                                                                     CATH domains
           Pfam domains (1) ---OKR_DC_1_N-1ordB01 B:4-102                                                                         -----OKR_DC_1-1ordB03 B:108-551                                                                                                                                                                                                                                                                                                                                                                                                                                  ------------------------OKR_DC_1_C-1ordB05 B:576-709                                                                                                          --------------------- Pfam domains (1)
           Pfam domains (2) ---OKR_DC_1_N-1ordB02 B:4-102                                                                         -----OKR_DC_1-1ordB04 B:108-551                                                                                                                                                                                                                                                                                                                                                                                                                                  ------------------------OKR_DC_1_C-1ordB06 B:576-709                                                                                                          --------------------- Pfam domains (2)
         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
                 1ord B   1 SSSLKIASTQEARQYFDTDRVVVDAVGSDFTDVGAVIAMDYETDVIDAADATKFGIPVFAVTKDAQAISADELKKIFHIIDLENKFDATVNAREIETAVNNYEDSILPPFFKSLKEYVSRGLIQFDCPGHQGGQYYRKHPAGREFYDFFGETVFRADLCNADVALGDLLIHEGPAVAAEKHAARVYNADKTYFVLGGSSNANNTVTSALVSNGDLVLFDRNNHKSVYNSALAMAGGRPVYLQTNRNPYGFIGGIYDSDFDEKKIRELAAKVDPERAKWKRPFRLAVIQLGTYDGTIYNAHEVVKRIGHLCDYIEFDSAWVGYEQFIPMMRNSSPLLIDDLGPEDPGIIVVQSVHKQQAGFSQTSQIHKKDSHIKGQLRYCDHKHFNNSFNLFMSTSPFYPMYAALDVNAAMQEGEAGRKLWHDLLITTIEARKKLIKAGSMFRPFVPPVVNGKKWEDGDTEDMANNIDYWRFEKGAKWHAYEGYGDNQYYVDPNKFMLTTPGINPETGDYEDFGVPATIVANYLRDHGIIPEKSDLNSILFLMTPAETPAKMNNLITQLLQLQRLIEEDAPLKQVLPSIYAANEERYNGYTIRELCQELHDFYKNNNTFTYQKRLFLREFFPEQGMLPYEARQEFIRNHNKLVPLNKIEGEIALEGALPYPPGVFCVAPGEKWSETAVKYFTILQDGINNFPGFAPEIQGVYFKQEGDKVVAYGEVYDAEVAKNDDRYNN 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

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 Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CheY (97)

Family: OKR_DC_1_N (3)

Lactobacillus sp. (strain 30a) (1)

1a	OKR_DC_1_N-1ordB01	B:4-102
1b	OKR_DC_1_N-1ordB02	B:4-102

Clan: PLP_aminotran (240)

Family: OKR_DC_1 (3)

Lactobacillus sp. (strain 30a) (1)

2a	OKR_DC_1-1ordB03	B:108-551
2b	OKR_DC_1-1ordB04	B:108-551

Clan: no clan defined [family: OKR_DC_1_C] (3)

Family: OKR_DC_1_C (3)

Lactobacillus sp. (strain 30a) (1)

3a	OKR_DC_1_C-1ordB05	B:576-709
3b	OKR_DC_1_C-1ordB06	B:576-709

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
		Cys A:127 - Pro A:128	[ RasMol ]
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		Pro A:661 - Pro A:662	[ RasMol ]
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		Tyr B:660 - Pro B:661	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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