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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  ORNITHINE TRANSCARBAMYLASE FROM ESCHERICHIA COLI
 
Authors :  J. F. Head, B. Seaton, L. Jin
Date :  23 May 97  (Deposition) - 27 May 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase, Anabolic, Urea Cycle, Carbamyl Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Jin, B. A. Seaton, J. F. Head
Crystal Structure At 2. 8 A Resolution Of Anabolic Ornithine Transcarbamylase From Escherichia Coli.
Nat. Struct. Biol. V. 4 622 1997
PubMed-ID: 9253409  |  Reference-DOI: 10.1038/NSB0897-622
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ORNITHINE TRANSCARBAMYLASE
    Chains: A, B, C
    EC Number: 2.1.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: ARGI
    Expression System Plasmid: PUC18
    Expression System Strain: TB2
    Expression System Taxid: 562
    Expression System Variant: DELTA ARGI-PYRB, ARGF-
    Expression System Vector Type: PLASMID
    Gene: ARGI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ORNITHINE CARBAMOYLTRANSFERASE, ORNITHINE TRANSCARBAMOYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1AKM)

(-) Sites  (0, 0)

(no "Site" information available for 1AKM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:274 -Pro A:275
2Leu B:274 -Pro B:275
3Leu C:274 -Pro C:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 3)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1AKM)

(-) 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:322
 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 d1akma1 A:1-150 Ornithine transcarbamoylase                                                                                                           d1akma2 A:151-333 Ornithine transcarbamoylase                                                                                                                                           SCOP domains
               CATH domains 1akmA01 A:1-135,A:319-332  [code=3.40.50.1370, no name defined]                                                                        1akmA02 A:136-318  [code=3.40.50.1370, no name defined]                                                                                                                                1akmA01       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh..hhhhhhhhhhhhhhhhhhhh..........eeeeee....hhhhhhhhhhhhhh..eeeee............hhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh....hhh.eeeee.....hhhhhhhhhhhhh..eeeee..hhh...hhhhhhhhhhhhhh..eeeee..hhhhh....eeee....-----------.hhhhhhh...hhhhhhh.....eeee..........hhhhhhhhh..........hhhh......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------CARBAMOY----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1akm A   1 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWV-----------RIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   |     -     | 250       260       270       280       290       300       310       320       330   
                                                                                                                                                                                                                                                                   234         246                                                                                       


Chain B from PDB  Type:PROTEIN  Length:322
 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 d1akmb1 B:1-150 Ornithine transcarbamoylase                                                                                                           d1akmb2 B:151-333 Ornithine transcarbamoylase                                                                                                                                           SCOP domains
               CATH domains 1akmB01 B:1-135,B:319-332  [code=3.40.50.1370, no name defined]                                                                        1akmB02 B:136-318  [code=3.40.50.1370, no name defined]                                                                                                                                1akmB01       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh..hhhhhhhhhhhhhhhhhhh...........eeeeee....hhhhhhhhhhhhh...eeeee............hhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhh.....hhh.eeeee.....hhhhhhhhhhhhh..eeeee..hhh...hhhhhhhhhhhhhh..eeeee..hhhhh....eeee....-----------.hhhhhhh...hhhhhhh.....eeee..........hhhhhhhhh..........hhhh......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------CARBAMOY----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1akm B   1 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWV-----------RIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   |     -     | 250       260       270       280       290       300       310       320       330   
                                                                                                                                                                                                                                                                   234         246                                                                                       


Chain C from PDB  Type:PROTEIN  Length:322
 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 d1akmc1 C:1-150 Ornithine transcarbamoylase                                                                                                           d1akmc2 C:151-333 Ornithine transcarbamoylase                                                                                                                                           SCOP domains
               CATH domains 1akmC01 C:1-135,C:319-332  [code=3.40.50.1370, no name defined]                                                                        1akmC02 C:136-318  [code=3.40.50.1370, no name defined]                                                                                                                                1akmC01       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh..hhhhhhhhhhhhhhhhhhh...........eeeeee....hhhhhhhhhhhhh...eeeee............hhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh....hhh.eeeee.....hhhhhhhhhhhhh..eeeee..hhh...hhhhhhhhhhhhhh..eeeee..hhhhh....eeee....-----------.hhhhhhh...hhhhhhh.....eeee..........hhhhhhhhh..........hhhh......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------CARBAMOY----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1akm C   1 SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWV-----------RIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK 333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   |     -     | 250       260       270       280       290       300       310       320       330   
                                                                                                                                                                                                                                                                   234         246
   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)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: [code=3.40.50.1370, no name defined] (91)
(-)
Escherichia coli. Organism_taxid: 562. (22)
1a1akmA01A:1-135,A:319-332
1b1akmA02A:136-318
1c1akmB02B:136-318
1d1akmC02C:136-318
1e1akmB01B:1-135,B:319-332
1f1akmC01C:1-135,C:319-332

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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: 1duv 2otc

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