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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH NDELTA-L-ORNITHINE-DIAMINOPHOSPHINYL-N-SULPHONIC ACID (PSORN)
 
Authors :  D. B. Langley, M. D. Templeton, B. A. Fields, R. E. Mitchell, C. A. Collyer
Date :  18 Jan 00  (Deposition) - 04 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  G,H,I
Keywords :  Enzyme-Inhibitor Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. B. Langley, M. D. Templeton, B. A. Fields, R. E. Mitchell, C. A. Collyer
Mechanism Of Inactivation Of Ornithine Transcarbamoylase By Ndelta -(N'-Sulfodiaminophosphinyl)-L-Ornithine, A True Transition State Analogue? Crystal Structure And Implications For Catalytic Mechanism.
J. Biol. Chem. V. 275 20012 2000
PubMed-ID: 10747936  |  Reference-DOI: 10.1074/JBC.M000585200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ORNITHINE TRANSCARBAMOYLASE
    Chains: G, H, I
    EC Number: 2.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: OCTASE-1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : GHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2PSQ3Ligand/IonNDELTA-(N'-SULPHODIAMINOPHOSPHINYL)-L-ORNITHINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER G:55 , THR G:56 , ARG G:57 , THR G:58 , ARG G:106 , LEU G:128 , HIS G:133 , GLN G:136 , ASN G:166 , ASN G:167 , ASP G:231 , SER G:235 , MET G:236 , CYS G:273 , LEU G:274 , ARG G:319 , HOH G:606 , GLN I:82 , HOH I:598BINDING SITE FOR RESIDUE PSQ G 401
2AC2SOFTWAREGLN G:82 , SER H:55 , THR H:56 , ARG H:57 , THR H:58 , ARG H:106 , HIS H:133 , GLN H:136 , ASN H:166 , ASN H:167 , ASP H:231 , SER H:235 , MET H:236 , CYS H:273 , LEU H:274 , ARG H:319 , HOH H:602 , HOH H:611BINDING SITE FOR RESIDUE PSQ H 402
3AC3SOFTWAREGLN H:82 , SER I:55 , THR I:56 , ARG I:57 , THR I:58 , ARG I:106 , HIS I:133 , GLN I:136 , ASN I:166 , ASN I:167 , ASP I:231 , SER I:235 , MET I:236 , CYS I:273 , LEU I:274 , ARG I:319 , HOH I:604 , HOH I:773BINDING SITE FOR RESIDUE PSQ I 403
4AC4SOFTWARELEU G:25 , ALA G:329 , LYS G:333 , HOH G:538 , HOH G:1149 , LYS H:151BINDING SITE FOR RESIDUE MPD G 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu G:274 -Pro G:275
2Leu H:274 -Pro H:275
3Leu I:274 -Pro I:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBAMOYLTRANSFERASEPS00097 Aspartate and ornithine carbamoyltransferases signature.OTC1_ECOLI52-59
 
 		  3G:51-58
H:51-58
I:51-58

(-) Exons   (0, 0)

(no "Exon" information available for 1DUV)

(-) 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 G from PDB  Type:PROTEIN  Length:333
 aligned with OTC1_ECOLI | P04391 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:333
                                    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   
           OTC1_ECOLI     2 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 334
               SCOP domains d1duvg1 G:1-150 Ornithine transcarbamoylase                                                                                                           d1duvg2 G:151-333 Ornithine transcarbamoylase                                                                                                                                           SCOP domains
               CATH domains 1duvG01 G:1-135,G:319-333  [code=3.40.50.1370, no name defined]                                                                        1duvG02 G:136-318  [code=3.40.50.1370, no name defined]                                                                                                                                1duvG01         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh....eeeee..hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhh...hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhh..eeeee.hhhhhhh...eeee..........hhhhhhhhhhhhhh.hhhhhhh......eeee.........hhhhhhhhhhh........hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------CARBAMOY----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1duv G   1 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 333
                                    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   


Chain H from PDB  Type:PROTEIN  Length:333
 aligned with OTC1_ECOLI | P04391 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:333
                                    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   
           OTC1_ECOLI     2 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 334
               SCOP domains d1duvh1 H:1-150 Ornithine transcarbamoylase                                                                                                           d1duvh2 H:151-333 Ornithine transcarbamoylase                                                                                                                                           SCOP domains
               CATH domains 1duvH01 H:1-135,H:319-333  [code=3.40.50.1370, no name defined]                                                                        1duvH02 H:136-318  [code=3.40.50.1370, no name defined]                                                                                                                                1duvH01         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh....eeeee..hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhh...hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhh..eeeee.hhhhhhh...eeee..........hhhhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhh........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------CARBAMOY----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1duv H   1 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 333
                                    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   


Chain I from PDB  Type:PROTEIN  Length:333
 aligned with OTC1_ECOLI | P04391 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:333
                                    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   
           OTC1_ECOLI     2 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 334
               SCOP domains d1duvi1 I:1-150 Ornithine transcarbamoylase                                                                                                           d1duvi2 I:151-333 Ornithine transcarbamoylase                                                                                                                                           SCOP domains
               CATH domains 1duvI01 I:1-135,I:319-333  [code=3.40.50.1370, no name defined]                                                                        1duvI02 I:136-318  [code=3.40.50.1370, no name defined]                                                                                                                                1duvI01         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh....eeeee..hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhh...hhhh.eeeee....hhhhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhhh..eeeee.hhhhhhh...eeee........hhhhhhhhhhhhhhhh.hhhhhhhh.....eeee.........hhhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------CARBAMOY----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1duv I   1 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 333
                                    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
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain G,H,I   (OTC1_ECOLI | P04391)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0016743    carboxyl- or carbamoyltransferase activity    Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004585    ornithine carbamoyltransferase activity    Catalysis of the reaction: carbamoyl phosphate + L-ornithine = phosphate + L-citrulline.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006526    arginine biosynthetic process    The chemical reactions and pathways resulting in the formation of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
    GO:0042450    arginine biosynthetic process via ornithine    The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006591    ornithine metabolic process    The chemical reactions and pathways involving ornithine, an amino acid only rarely found in proteins, but which is important in living organisms as an intermediate in the reactions of the urea cycle and in arginine biosynthesis.
    GO:0000050    urea cycle    The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        OTC1_ECOLI | P04391: 1akm 2otc

(-) Related Entries Specified in the PDB File

1oth 1OTH CONTAINS THE HUMAN PROTEIN COMPLEXED WITH A RELATED INHIBITOR
2otc 2OTC CONTAINS THE SAME PROTEIN COMPLEXED WITH A RELATED INHIBITOR