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(-) Description

Title :  STRUCTURE AND A PROPOSED MECHANISM FOR ORNITHINE CYCLODEAMINASE FROM PSEUDOMONAS PUTIDA
 
Authors :  S. Alam, J. L. Goodman, S. Wang, F. J. Ruzicka, P. A. Frey, J. E. Wedekind
Date :  03 Aug 04  (Deposition) - 09 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Deaminase, Binds Nad+, Binds L-Ornithine, Binds L-Pro, 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
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric/Biological Unit (4, 25)
No.NameCountTypeFull Name
1MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3NA2Ligand/IonSODIUM ION
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:224 , VAL A:225 , GLY A:227 , SER A:293 , HOH A:992 , HOH A:994BINDING SITE FOR RESIDUE NA A 911
2AC2SOFTWAREALA B:224 , VAL B:225 , GLY B:227 , SER B:293 , HOH B:1104 , HOH B:1105BINDING SITE FOR RESIDUE NA B 912
3AC3SOFTWARELYS A:331 , HOH A:1021 , HOH A:1143 , 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:1080 , HOH B:1087 , HOH B:1096 , HOH B:1097 , HOH B:1101 , HOH B:1109 , HOH B:1143 , HOH B:1144BINDING SITE FOR RESIDUE NAD B 801
4AC4SOFTWARETHR 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 , HOH A:971 , HOH A:973 , HOH A:977 , HOH A:998 , HOH A:1002 , HOH A:1003 , HOH A:1004 , HOH A:1016 , HOH A:1018 , HOH A:1211 , LYS B:331BINDING SITE FOR RESIDUE NAD A 802
5AC5SOFTWAREGLN A:38 , ALA A:39 , ALA A:61 , ASP A:62 , LYS A:63BINDING SITE FOR RESIDUE MPD A 901
6AC6SOFTWAREALA A:39 , HOH A:1149 , HOH A:1150 , LEU B:216 , PRO B:218 , SER B:286 , VAL B:288 , HOH B:992BINDING SITE FOR RESIDUE MPD A 902
7AC7SOFTWARESER B:64 , ARG B:65 , ALA B:92 , ASP B:93 , VAL B:100 , LEU B:308 , HOH B:1254 , HOH B:1255 , HOH B:1256BINDING SITE FOR RESIDUE MPD B 903
8AC8SOFTWARETYR A:3 , ALA A:311 , GLU A:312 , GLY A:315 , MSE A:316BINDING SITE FOR RESIDUE MPD A 904
9AC9SOFTWARETYR B:3 , ALA B:311 , GLU B:312 , GLY B:315 , MSE B:316BINDING SITE FOR RESIDUE MPD B 905

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U7H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U7H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U7H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U7H)

(-) Exons   (0, 0)

(no "Exon" information available for 1U7H)

(-) 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:341
 aligned with Q88H32_PSEPK | Q88H32 from UniProtKB/TrEMBL  Length:350

    Alignment length: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 
         Q88H32_PSEPK     2 TYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPVADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFSHTRGRAG 342
               SCOP domains d1u7ha_ A: Ornithine cyclodeaminase                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1u7hA01 A:2-125,A:296-342 ornithine cyclodeaminase, domain 1                                                                1u7hA02 A:126-295 NAD(P)-binding Rossmann-like Domain                                                                                                                     1u7hA01 A:2-125,A:296-342                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeeeeeee...eeeeeeeeehhhhhhhh.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.....eeee..hhhhhhh...eeee......eeeeehhhhh....eeee........eeehhhhhhh.eeee.hhhhhhhhhhhhhh......eehhhhhh............eeee...hhhhhhhhhhhhhhhhhh....ee.............hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7h A   2 TYFIDVPTmSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELmPVADKSRYAFKYVNGHPANTARNLHTVmAFGVLADVDSGYPVLLSELTIATALRTAATSLmAAQALARPNARKmALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDmLEPGmHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGmGTKIDLVPWVEDDPKDLFSHTRGRAG 342
                                    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:340
 aligned with Q88H32_PSEPK | Q88H32 from UniProtKB/TrEMBL  Length:350

    Alignment length:340
                                    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
         Q88H32_PSEPK     1 MTYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPVADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFSHTRGR 340
               SCOP domains d1u7hb_ B: Ornithine cyclodeaminase                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1u7hB01 B:1-125,B:296-340 ornithine cyclodeaminase, domain 1                                                                 1u7hB02 B:126-295 NAD(P)-binding Rossmann-like Domain                                                                                                                     1u7hB01 B:1-125,B:296-340                     CATH domains
           Pfam domains (1) ------OCD_Mu_crystall-1u7hB01 B:7-315                                                                                                                                                                                                                                                                                      ------------------------- Pfam domains (1)
           Pfam domains (2) ------OCD_Mu_crystall-1u7hB02 B:7-315                                                                                                                                                                                                                                                                                      ------------------------- Pfam domains (2)
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeeeeeee...eeeeeeeee.hhhhhhh...eeeeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhh.....eeee..hhhhhhh...eeee......eeeeehhhhh....eeee........eeehhhhhhh.eeee.hhhhhhhhhhhhhh......eehhhhhh............eeee...hhhhhhhhhhhhhhhhhhhh..eee............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7h B   1 MTYFIDVPTmSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELmPVADKSRYAFKYVNGHPANTARNLHTVmAFGVLADVDSGYPVLLSELTIATALRTAATSLmAAQALARPNARKmALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYATIITPDmLEPGmHLNAVGGDCPGKTELHADVLRNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRGmGTKIDLVPWVEDDPKDLFSHTRGR 340
                                    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
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (2, 2)

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.

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  1u7h
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        Q88H32_PSEPK | Q88H32: 1x7d

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