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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI ARGININOSUCCINATE SYNTHETASE IN COMPLEX WITH ATP AND CITRULLINE
 
Authors :  C. T. Lemke, P. L. Howell
Date :  27 Dec 01  (Deposition) - 17 Apr 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  N-Type Atp Pyrophosphatase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. T. Lemke, P. L. Howell
Substrate Induced Conformational Changes In Argininosuccinate Synthetase
J. Biol. Chem. V. 277 13074 2002
PubMed-ID: 11809762  |  Reference-DOI: 10.1074/JBC.M112436200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININOSUCCINATE SYNTHETASE
    Chains: A
    EC Number: 6.3.4.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BB101
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARGG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CIR2Ligand/IonCITRULLINE
3GAI2Ligand/IonGUANIDINE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CIR8Ligand/IonCITRULLINE
3GAI8Ligand/IonGUANIDINE
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:262 , ARG A:269 , HOH A:595BINDING SITE FOR RESIDUE PO4 A 456
2AC2SOFTWAREALA A:16 , PHE A:17 , SER A:18 , GLY A:20 , LEU A:21 , ASP A:22 , THR A:23 , TYR A:40 , ALA A:42 , ARG A:106 , LEU A:113 , ASP A:127 , GLY A:128 , SER A:129 , PHE A:139 , ASP A:193 , CIR A:459 , HOH A:572 , HOH A:614 , HOH A:631BINDING SITE FOR RESIDUE ATP A 457
3AC3SOFTWARETYR A:98 , THR A:102 , PRO A:103 , ASN A:134 , ARG A:138 , SER A:191 , ASP A:193 , THR A:200 , GLU A:202 , GLU A:279 , TYR A:291 , CIR A:459BINDING SITE FOR RESIDUE CIR A 458
4AC4SOFTWARETHR A:130 , GLY A:133 , ASN A:134 , ASP A:135 , GLU A:202 , SER A:287 , ATP A:457 , CIR A:458 , HOH A:500BINDING SITE FOR RESIDUE CIR A 459
5AC5SOFTWAREMET A:60 , ALA A:64 , GLU A:65 , ASN A:210 , SER A:211BINDING SITE FOR RESIDUE GAI A 460
6AC6SOFTWARETHR A:1 , ASP A:399 , HOH A:584 , HOH A:609BINDING SITE FOR RESIDUE GAI A 461

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KP3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KP3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KP3)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGININOSUCCIN_SYN_1PS00564 Argininosuccinate synthase signature 1.ASSY_ECOLI17-25  1A:16-24
2ARGININOSUCCIN_SYN_2PS00565 Argininosuccinate synthase signature 2.ASSY_ECOLI129-140  1A:128-139
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARGININOSUCCIN_SYN_1PS00564 Argininosuccinate synthase signature 1.ASSY_ECOLI17-25  4A:16-24
2ARGININOSUCCIN_SYN_2PS00565 Argininosuccinate synthase signature 2.ASSY_ECOLI129-140  4A:128-139

(-) Exons   (0, 0)

(no "Exon" information available for 1KP3)

(-) Sequences/Alignments

Asymmetric 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:439
 aligned with ASSY_ECOLI | P0A6E4 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:446
                                    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       351       361       371       381       391       401       411       421       431       441      
           ASSY_ECOLI     2 TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACGFDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVRFEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALLHIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEVTLELRRGNDYSILNTVSENLTYKPERLTMEKGDSVFSPDDRIGQLTMRNLDITDTREKLFGYAKTGLLSSSAASGVPQVENLENKGQ 447
               SCOP domains d1kp3a1 A:1-188 Argininosuccinate synthetase, N-terminal domain                                                                                                                             d1kp3a2 A:189-446 Argininosuccinate synthetase, C-terminal domain                                                                                                                                                                                                  SCOP domains
               CATH domains 1kp3A01 A:1-72,A:101-188                                                1kp3A02 A:73-100,A:189-375  1kp3A01 A:1-72,A:101-188 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1          1kp3A02 A:73-100,A:189-375 Argininosuccinate synthetase, chain A, domain 2                                                                                                                 1kp3A03 A:       376-440  [code=1.10.287.400, no name defined]   ------ CATH domains
               Pfam domains -------------Arginosuc_synth-1kp3A01 A:14-414                                                                                                                                                                                                                                                                                                                                                                                 -------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhh..eeeeeeee.........hhhhhhhhhh....eeeeehhhhhhhhhhhhhhhh....ee..ee..hhhhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhhhhhhhhhh............eeeee..eeeee.hhhhh...hhhhh.................eeeeeeee..eeeee......hhhhhhhhhhhhhhh.....eeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeeeee..........-------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------ARGININOS-------------------------------------------------------------------------------------------------------ARGININOSUCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kp3 A   1 TTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACGFDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVRFEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALLHIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEVTLELRRGNDYSILNTVSENLTYKPER-------SVFSPDDRIGQLTMRNLDITDTREKLFGYAKTGLLSSSAASGVPQVENLENKGQ 446
                                    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       350       360       370       380    |    -  |    400       410       420       430       440      
                                                                                                                                                                                                                                                                                                                                                                                                                          385     393
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (ASSY_ECOLI | P0A6E4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004055    argininosuccinate synthase activity    Catalysis of the reaction: ATP + L-citrulline + L-aspartate = AMP + diphosphate + (N(omega)-L-arginino)succinate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0000053    argininosuccinate metabolic process    The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate.
    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: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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ASSY_ECOLI | P0A6E4: 1k92 1k97 1kp2

(-) Related Entries Specified in the PDB File

1k92 1K92 IS E. COLI ARGININOSUCCINATE SYNTHETASE
1k97 1K97 IS E. COLI ARGININOSUCCINATE SYNTHETASE IN COMPLEX WITH CITRULLINE AND ASPARTATE
1kp2 1KP2 IS E. COLI ARGININOSUCCINATE SYNTHETASE IN COMPLEX WITH ATP