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(-) Description

Title :  CRYSTAL STRUCTURE OF A NEW TRANSCARBAMYLASE FROM THE ANAEROBIC BACTERIUM BACTEROIDES FRAGILIS AT 2.0 A RESOLUTION
 
Authors :  D. Shi, R. Gallegos, J. Deponte Iii, H. Morizono, X. Yu, N. M. Allewell, M. Tuchman
Date :  15 Aug 01  (Deposition) - 17 Jul 02  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  X,Y,Z
Keywords :  Alpha/Beta Topology, Two Domains, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Shi, R. Gallegos, J. Deponte 3Rd. , H. Morizono, X. Yu, N. M. Allewell, M. Malamy, M. Tuchman
Crystal Structure Of A Transcarbamylase-Like Protein From The Anaerobic Bacterium Bacteroides Fragilis At 2. 0 A Resolution.
J. Mol. Biol. V. 320 899 2002
PubMed-ID: 12095263  |  Reference-DOI: 10.1016/S0022-2836(02)00539-9

(-) Compounds

Molecule 1 - TRANSCARBAMYLASE
    Chains: X, Y, Z
    EC Number: 2.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 817

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : XYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER X:47 , LEU X:48 , ARG X:49 , THR X:50 , ARG X:110BINDING SITE FOR RESIDUE PO4 X 501
2AC2SOFTWARESER Y:47 , LEU Y:48 , ARG Y:49 , THR Y:50 , ARG Y:110BINDING SITE FOR RESIDUE PO4 Y 502
3AC3SOFTWARESER Z:46 , SER Z:47 , LEU Z:48 , ARG Z:49 , THR Z:50BINDING SITE FOR RESIDUE PO4 Z 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JS1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu X:275 -Pro X:276
2Leu Y:275 -Pro Y:276
3Leu Z:275 -Pro Z:276

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JS1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JS1)

(-) Exons   (0, 0)

(no "Exon" information available for 1JS1)

(-) 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 X from PDB  Type:PROTEIN  Length:324
 aligned with AOTC_BACTN | Q8A1E9 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:324
                                                                                                                                                                                                                                                                                                                                                       318      
                                    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       | -    
           AOTC_BACTN     1 MKKFTCVQDIGDLKSALAEAFEIQKDRFKYVELGRNKTLMMIFFNSSLRTRLSTQKAALNLGMNVMVLDINQGAWKLETERGVIMDGDKPEHLLEAIPVMGCYCDIIGVRSFARFEDRDFDYQETILNQFIQYSGRPVFSMEAATRHPLQSFADLITIEEYKKTARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYDFVITHPEGYELAPQFVGNAKVEYDQMKAFEGADFIYAKNWAAYTGDNYGQILSKDREWTVSDRQMAVTNNAFFMHCLPVRRNMIVTDDVIESPQSIVIPEAANREISATVVLKRLIEGLE------   -
               SCOP domains d1js1x1 X:1-163 Transcarbamylase-like protein                                                                                                                      d1js1x2 X:164-324 Transcarbamylase-like protein                                                                                                                   SCOP domains
               CATH domains 1js1X01 X:1-147,X:302-324  [code=3.40.50.1370, no name defined]                                                                                    --1js1X02 X:150-301  [code=3.40.50.1370, no name defined]                                                                                                 1js1X01                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh...........eeeeee....hhhhhhhhhhhhhh..eeeeee.hhhhh.ee............eehhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhh...eeeee.......hhhhhh..eee.hhhhhhh...eeee.......................hhhhhh.....eee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1js1 X   1 MKKFTCVQDIGDLKSALAESFEIKKDRFKYVELGRNKTLLMIFFNSSLRTRLSTQKAALNLGMNVIVLDINQGAWKLETERGVIMDGDKPEHLLEAIPVMGCYCDIIGVRSFARFENREYDYNEVIINQFIQHSGRPVFSMEAATRHPLQSFADLITIEEYKKTARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYEFVITHPEGYELDPKFVGNARVEYDQMKAFEGADFIYAKNWAAYTGDNYGQILSTDRNWTVGDRQMAVTNNAYFMHCLPVRRNMIVTDDVIESPQSIVIPEAANREISATVVLKRLLENLPHHHHHH 324
                                    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    


Chain Y from PDB  Type:PROTEIN  Length:318
 aligned with AOTC_BACTN | Q8A1E9 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:318
                                    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        
           AOTC_BACTN     1 MKKFTCVQDIGDLKSALAEAFEIQKDRFKYVELGRNKTLMMIFFNSSLRTRLSTQKAALNLGMNVMVLDINQGAWKLETERGVIMDGDKPEHLLEAIPVMGCYCDIIGVRSFARFEDRDFDYQETILNQFIQYSGRPVFSMEAATRHPLQSFADLITIEEYKKTARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYDFVITHPEGYELAPQFVGNAKVEYDQMKAFEGADFIYAKNWAAYTGDNYGQILSKDREWTVSDRQMAVTNNAFFMHCLPVRRNMIVTDDVIESPQSIVIPEAANREISATVVLKRLIEGLE 318
               SCOP domains d1js1y1 Y:1-163 Transcarbamylase-like protein                                                                                                                      d1js1y2 Y:164-318 Transcarbamylase-like protein                                                                                                             SCOP domains
               CATH domains 1js1Y01 Y:1-147,Y:302-318  [code=3.40.50.1370, no name defined]                                                                                    --1js1Y02 Y:150-301  [code=3.40.50.1370, no name defined]                                                                                                 1js1Y01           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhhhhhh...........eeeeee....hhhhhhhhhhhhhh..eeeeee.......ee............eehhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhh....eeeee.......hhhhhh..ee..hhhhhhh...eeee......hhhhh......hhhhh.hhhhhh.....eee...........hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1js1 Y   1 MKKFTCVQDIGDLKSALAESFEIKKDRFKYVELGRNKTLLMIFFNSSLRTRLSTQKAALNLGMNVIVLDINQGAWKLETERGVIMDGDKPEHLLEAIPVMGCYCDIIGVRSFARFENREYDYNEVIINQFIQHSGRPVFSMEAATRHPLQSFADLITIEEYKKTARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYEFVITHPEGYELDPKFVGNARVEYDQMKAFEGADFIYAKNWAAYTGDNYGQILSTDRNWTVGDRQMAVTNNAYFMHCLPVRRNMIVTDDVIESPQSIVIPEAANREISATVVLKRLLENLP 318
                                    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        


Chain Z from PDB  Type:PROTEIN  Length:318
 aligned with AOTC_BACTN | Q8A1E9 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:318
                                    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        
           AOTC_BACTN     1 MKKFTCVQDIGDLKSALAEAFEIQKDRFKYVELGRNKTLMMIFFNSSLRTRLSTQKAALNLGMNVMVLDINQGAWKLETERGVIMDGDKPEHLLEAIPVMGCYCDIIGVRSFARFEDRDFDYQETILNQFIQYSGRPVFSMEAATRHPLQSFADLITIEEYKKTARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYDFVITHPEGYELAPQFVGNAKVEYDQMKAFEGADFIYAKNWAAYTGDNYGQILSKDREWTVSDRQMAVTNNAFFMHCLPVRRNMIVTDDVIESPQSIVIPEAANREISATVVLKRLIEGLE 318
               SCOP domains d1js1z1 Z:1-163 Transcarbamylase-like protein                                                                                                                      d1js1z2 Z:164-318 Transcarbamylase-like protein                                                                                                             SCOP domains
               CATH domains 1js1Z01 Z:1-147,Z:302-318  [code=3.40.50.1370, no name defined]                                                                                    --1js1Z02 Z:150-301  [code=3.40.50.1370, no name defined]                                                                                                 1js1Z01           CATH domains
           Pfam domains (1) -OTCace_N-1js1Z04 Z:2-161                                                                                                                                        -----OTCace-1js1Z01 Z:167-313                                                                                                                           ----- Pfam domains (1)
           Pfam domains (2) -OTCace_N-1js1Z05 Z:2-161                                                                                                                                        -----OTCace-1js1Z02 Z:167-313                                                                                                                           ----- Pfam domains (2)
           Pfam domains (3) -OTCace_N-1js1Z06 Z:2-161                                                                                                                                        -----OTCace-1js1Z03 Z:167-313                                                                                                                           ----- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh...........eeeeee....hhhhhhhhhhhhhh..eeeeee.......ee............eehhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhh...eeeee.......hhhhhh..ee..hhhhhhh...eeee......hhhhh............hhhhhh.....eee...........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1js1 Z   1 MKKFTCVQDIGDLKSALAESFEIKKDRFKYVELGRNKTLLMIFFNSSLRTRLSTQKAALNLGMNVIVLDINQGAWKLETERGVIMDGDKPEHLLEAIPVMGCYCDIIGVRSFARFENREYDYNEVIINQFIQHSGRPVFSMEAATRHPLQSFADLITIEEYKKTARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYEFVITHPEGYELDPKFVGNARVEYDQMKAFEGADFIYAKNWAAYTGDNYGQILSTDRNWTVGDRQMAVTNNAYFMHCLPVRRNMIVTDDVIESPQSIVIPEAANREISATVVLKRLLENLP 318
                                    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
   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  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: OTCace] (48)
(-)
Clan: no clan defined [family: OTCace_N] (48)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X,Y,Z   (AOTC_BACTN | Q8A1E9)
molecular function
    GO:0043857    N-acetylornithine carbamoyltransferase activity    Catalysis of the reaction: N(2)-acetyl-L-ornithine + carbamoyl phosphate = N(2)-acetyl-L-citrulline + H(+) + phosphate.
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0004070    aspartate carbamoyltransferase activity    Catalysis of the reaction: L-aspartate + carbamoyl phosphate = N-carbamoyl-L-aspartate + H(+) + phosphate.
    GO:0016743    carboxyl- or carbamoyltransferase activity    Catalysis of the transfer of a carboxyl- or carbamoyl group from one compound (donor) to another (acceptor).
    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:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    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: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

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