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Title :   CRYSTAL STRUCTURE ANALYSIS OF ORNITHINE CYCLODEAMINASE COMPLEXED WITH NAD AND ORNITHINE TO 1.6 ANGSTROMS

Authors :   S. Alam, J. L. Goodman, S. Wang, F. J. Ruzicka, P. A. Frey, J. E. Wedekind

Date :   13 Aug 04 (Deposition) - 09 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Deaminase, Binds Nad+, Binds L-Ornithine, Binds L-Proline, 2 Helix Bundle, Beta Barrel, Rossmann Fold, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. L. Goodman, S. Wang, S. Alam, F. J. Ruzicka, P. A. Frey, J. E. Wedekind
Ornithine Cyclodeaminase: Structure, Mechanism Of Action, And Implications For The U-Crystallin Family
Biochemistry V. 43 13883 2004
PubMed-ID: 15518536 | Reference-DOI: 10.1021/BI048207I

Molecule 1 - ORNITHINE CYCLODEAMINASE
	Chains	:	A, B
	EC Number	:	4.3.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A(+) AND PET-21A-OCD
	Expression System Strain	:	ROSETTA(DE3) AND D834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ORNITHINE CYCLASE (DEAMINATING)
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 29)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
4	NA	2	Ligand/Ion	SODIUM ION
5	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6	ORN	2	Ligand/Ion	L-ORNITHINE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:224 , VAL A:225 , GLY A:227 , SER A:293 , HOH A:1513 , HOH A:1879	BINDING SITE FOR RESIDUE NA A 1501
02	AC2	SOFTWARE	ALA B:224 , VAL B:225 , GLY B:227 , SER B:293 , HOH B:3176 , HOH B:3315	BINDING SITE FOR RESIDUE NA B 1502
03	AC3	SOFTWARE	LYS A:331 , ORN A:1102 , HOH A:1516 , HOH A:1668 , THR B:84 , ARG B:112 , THR B:113 , GLY B:138 , ALA B:139 , GLN B:140 , ASP B:161 , THR B:162 , VAL B:201 , THR B:202 , ALA B:203 , ILE B:210 , VAL B:225 , GLY B:226 , ASP B:228 , LYS B:232 , SER B:293 , VAL B:294 , GLY B:295 , HOH B:3165 , HOH B:3166 , HOH B:3170 , HOH B:3209 , HOH B:3223 , HOH B:3323 , HOH B:3387 , HOH B:3538	BINDING SITE FOR RESIDUE NAD B 1301
04	AC4	SOFTWARE	THR A:84 , ARG A:112 , THR A:113 , GLY A:138 , ALA A:139 , GLN A:140 , ASP A:161 , THR A:162 , VAL A:201 , THR A:202 , ALA A:203 , ILE A:210 , VAL A:225 , GLY A:226 , ASP A:228 , LYS A:232 , SER A:293 , VAL A:294 , GLY A:295 , ORN A:1101 , HOH A:1503 , HOH A:1504 , HOH A:1512 , HOH A:1519 , HOH A:1559 , HOH A:1598 , HOH A:1610 , HOH A:1686 , HOH A:1695 , HOH A:1801 , LYS B:331	BINDING SITE FOR RESIDUE NAD A 1302
05	AC5	SOFTWARE	ARG A:45 , VAL A:54 , GLU A:56 , LYS A:69 , VAL A:71 , ASN A:72 , GLY A:73 , VAL A:85 , ARG A:112 , ASP A:228 , VAL A:294 , GLY A:295 , NAD A:1302 , HOH A:1558 , HOH A:1642 , HOH A:1695	BINDING SITE FOR RESIDUE ORN A 1101
06	AC6	SOFTWARE	HOH A:1611 , ARG B:45 , VAL B:54 , GLU B:56 , MSE B:58 , LYS B:69 , ASN B:72 , GLY B:73 , VAL B:85 , ARG B:112 , ASP B:228 , VAL B:294 , GLY B:295 , NAD B:1301 , HOH B:3207	BINDING SITE FOR RESIDUE ORN A 1102
07	AC7	SOFTWARE	GLN A:283 , SER A:284 , GLN A:287 , ARG A:338 , HOH A:1793 , HIS B:15 , GLU B:176 , TYR B:177 , HOH B:3259	BINDING SITE FOR RESIDUE MES B 3158
08	AC8	SOFTWARE	GLN A:38 , ALA A:39 , PHE A:40 , ASP A:62 , LYS A:63 , MPD A:1402	BINDING SITE FOR RESIDUE MPD A 1401
09	AC9	SOFTWARE	GLN A:38 , ALA A:39 , MPD A:1401 , LEU B:216 , ASN B:242 , SER B:286 , HOH B:3440	BINDING SITE FOR RESIDUE MPD A 1402
10	BC1	SOFTWARE	SER A:64 , ARG A:65 , LEU A:91 , ASP A:93 , VAL A:100 , HOH A:1592	BINDING SITE FOR RESIDUE MPD A 1403
11	BC2	SOFTWARE	TYR A:3 , ALA A:311 , GLU A:312 , MSE A:316	BINDING SITE FOR RESIDUE MPD A 1404
12	BC3	SOFTWARE	TYR B:3 , ALA B:311 , GLU B:312 , GLY B:315 , MSE B:316	BINDING SITE FOR RESIDUE MPD B 1405
13	BC4	SOFTWARE	SER B:64 , ARG B:65 , ALA B:92 , ASP B:93 , VAL B:100 , LEU B:308 , HOH B:3267 , HOH B:3513	BINDING SITE FOR RESIDUE MPD B 1406

(no "SS Bond" information available for 1X7D)

(no "Cis Peptide Bond" information available for 1X7D)

(no "SAP(SNP)/Variant" information available for 1X7D)

(no "PROSITE Motif" information available for 1X7D)

(no "Exon" information available for 1X7D)

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:340
 aligned with Q88H32_PSEPK | Q88H32 from UniProtKB/TrEMBL  Length:350

    Alignment length:340
                                    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
         Q88H32_PSEPK     2 TYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPVADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFSHTRGRA 341
               SCOP domains d1x7da_ A: Ornithine cyclodeaminase                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1x7dA01 A:2-125,A:296-341 ornithine cyclodeaminase, domain 1                                                                1x7dA02 A:126-295 NAD(P)-binding Rossmann-like Domain                                                                                                                     1x7dA01 A:2-125,A:296-341                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeeeeeee...eeeeeeeee.hhhhhhh...eeeeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.....eeee..hhhhhhh...eeee......eeeeehhhhh....eeee........eeehhhhhhh.eeee.hhhhhhhhhhhhhh......eehhhhhh............eeee...hhhhhhhhhhhhhhhhhh....ee.............hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x7d A   2 TYFIDVPTmSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELmPVADKSRYAFKYVNGHPANTARNLHTVmAFGVLADVDSGYPVLLSELTIATALRTAATSLmAAQALARPNARKmALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDmLEPGmHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGmGTKIDLVPWVEDDPKDLFSHTRGRA 341
                                    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
                                   10-MSE                                          58-MSE                      86-MSE                          119-MSE      132-MSE                                                                            215-MSE|                                                                                             316-MSE                     
                                                                                                                                                                                                                                                    220-MSE

Chain B from PDB  Type:PROTEIN  Length:339
 aligned with Q88H32_PSEPK | Q88H32 from UniProtKB/TrEMBL  Length:350

    Alignment length:339
                                    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         
         Q88H32_PSEPK     2 TYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPVADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFSHTRGR 340
               SCOP domains d1x7db_ B: Ornithine cyclodeaminase                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1x7dB01 B:2-125,B:296-340 ornithine cyclodeaminase, domain 1                                                                1x7dB02 B:126-295 NAD(P)-binding Rossmann-like Domain                                                                                                                     1x7dB01 B:2-125,B:296-340                     CATH domains
           Pfam domains (1) -----OCD_Mu_crystall-1x7dB01 B:7-315                                                                                                                                                                                                                                                                                      ------------------------- Pfam domains (1)
           Pfam domains (2) -----OCD_Mu_crystall-1x7dB02 B:7-315                                                                                                                                                                                                                                                                                      ------------------------- Pfam domains (2)
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeeeeeee...eeeeeeeee.hhhhhhh...eeeeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.....eeee..hhhhhhh...eeee......eeeeehhhhh....eeee........eeehhhhhhh.eeee.hhhhhhhhhhhhhh......eehhhhhh............eeee...hhhhhhhhhhhhhhhhhhhh..ee............hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x7d B   2 TYFIDVPTmSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELmPVADKSRYAFKYVNGHPANTARNLHTVmAFGVLADVDSGYPVLLSELTIATALRTAATSLmAAQALARPNARKmALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDmLEPGmHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGmGTKIDLVPWVEDDPKDLFSHTRGR 340
                                    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         
                                   10-MSE                                          58-MSE                      86-MSE                          119-MSE      132-MSE                                                                            215-MSE|                                                                                             316-MSE                    
                                                                                                                                                                                                                                                    220-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Ornithine cyclodeaminase-like (4)

Protein domain: Ornithine cyclodeaminase (2)

Pseudomonas putida [TaxId: 303] (2)

1a	d1x7da_	A:
1b	d1x7db_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: ornithine cyclodeaminase, domain 1 (2)

Homologous Superfamily: ornithine cyclodeaminase, domain 1 (2)

Pseudomonas putida. Organism_taxid: 303. (2)

1a	1x7dA01	A:2-125,A:296-341
1b	1x7dB01	B:2-125,B:296-340

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Pseudomonas putida. Organism_taxid: 303. (5)

2a	1x7dA02	A:126-295
2b	1x7dB02	B:126-295

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: OCD_Mu_crystall (2)

Pseudomonas putida (strain KT2440) (2)

1a	OCD_Mu_crystall-1x7dB01	B:7-315
1b	OCD_Mu_crystall-1x7dB02	B:7-315

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q88H32_PSEPK | Q88H32)

molecular function
	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:0000166		nucleotide binding		Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Asymmetric/Biological Unit
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	1x7d
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	Q88H32_PSEPK \| Q88H32	:	1u7h

1u7h	CRYSTAL STRUCTURE OF ORNITHINE CYCLODEAMINASE COMPLEXED WITH NAD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 29)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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