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(-) Description

Title :  CRYSTAL STRUCTURE OF ALLANTOATE-AMIDOHYDROLASE FROM E.COLI K12 IN COMPLEX WITH SUBSTRATE ALLANTOATE
 
Authors :  R. Agarwal, S. Swaminathan, S. K. Burley, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  08 Mar 05  (Deposition) - 22 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Allantoate-Amidohydrolase, Allantoate, Allc, Purine Catabolism, Allantoin Utilization, T1507, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. K. Burley, S. Swaminathan
Structural Analysis Of A Ternary Complex Of Allantoate Amidohydrolase From Escherichia Coli Reveals Its Mechanics.
J. Mol. Biol. V. 368 450 2007
PubMed-ID: 17362992  |  Reference-DOI: 10.1016/J.JMB.2007.02.028

(-) Compounds

Molecule 1 - ALLANTOATE AMIDOHYDROLASE
    Chains: A, B
    EC Number: 3.5.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: TOPO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALLC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
11AL1Ligand/IonALLANTOATE ION
2SO42Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:83 , ASP A:94 , HIS A:192 , ZN A:512 , HOH A:629 , HOH A:631BINDING SITE FOR RESIDUE ZN A 511
2AC2SOFTWAREASP A:94 , GLU A:129 , HIS A:384 , ZN A:511 , HOH A:631BINDING SITE FOR RESIDUE ZN A 512
3AC3SOFTWAREHIS B:83 , ASP B:94 , HIS B:192 , ZN B:514 , HOH B:590 , HOH B:591BINDING SITE FOR RESIDUE ZN B 513
4AC4SOFTWAREASP B:94 , GLU B:129 , GLN B:195 , HIS B:384 , ZN B:513 , HOH B:591BINDING SITE FOR RESIDUE ZN B 514
5AC5SOFTWAREGLN A:215 , ARG A:217 , ARG A:290 , ALA A:358 , GLY A:359 , HIS B:228 , 1AL B:516BINDING SITE FOR RESIDUE SO4 A 513
6AC6SOFTWAREGLN B:215 , ARG B:217 , ARG B:290 , ALA B:358 , GLY B:359 , HOH B:534BINDING SITE FOR RESIDUE SO4 B 515
7AC7SOFTWAREARG A:217 , ARG A:290 , HIS A:384 , SO4 A:513 , HIS B:228 , ASN B:277 , VAL B:278 , HOH B:552BINDING SITE FOR RESIDUE 1AL B 516

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z2L)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:260 -Pro A:261
2Arg A:272 -Pro A:273
3Asp B:260 -Pro B:261
4Arg B:272 -Pro B:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z2L)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z2L)

(-) 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:411
 aligned with ALLC_ECOLI | P77425 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:411
                                    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       390       400       410 
           ALLC_ECOLI     1 MITHFRQAIEETLPWLSSFGADPAGGMTRLLYSPEWLETQQQFKKRMAASGLETRFDEVGNLYGRLNGTEYPQEVVLSGSHIDTVVNGGNLDGQFGALAAWLAIDWLKTQYGAPLRTVEVVAMAEEEGSRFPYVFWGSKNIFGLANPDDVRNICDAKGNSFVDAMKACGFTLPNAPLTPRQDIKAFVELHIEQGCVLESNGQSIGVVNAIVGQRRYTVTLNGESNHAGTTPMGYRRDTVYAFSRICHQSVEKAKRMGDPLVLTFGKVEPRPNTVNVVPGKTTFTIDCRHTDAAVLRDFTQQLENDMRAICDEMDIGIDIDLWMDEEPVPMNKELVATLTELCEREKLNYRVMHSGAGHDAQIFAPRVPTCMIFIPSINGISHNPAERTNITDLAEGVKTLALMLYQLAWQK 411
               SCOP domains -d1z2la1 A:4-212,A:330-413 Allantoate amidohydrolase AllC catalytic domain                                                                                                                                        d1z2la2 A:213-329 Allantoate amidohydrolase AllC                                                                     d1z2la1 A:4-212,A:330-413 Allantoate amidohydrolase AllC catalytic domain            SCOP domains
               CATH domains 1z2lA01 A:3-213,A:329-413 Zn peptidases                                                                                                                                                                            1z2lA02 A:214-328  [code=3.30.70.360, no name defined]                                                             1z2lA01 A:3-213,A:329-413 Zn peptidases                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..eeee.....eeeee....eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhh...eeeeeeee...........hhhhhhhh...hhhhh.........hhhhhhhhh..............eeeeeeeee...hhhhhh...eeeeeee.eeeeeeeeee...ee....hhhhh.hhhhhhhhhhhhhhhhhhhhh...eee...eeee.....ee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..ee.hhhhhhhhhhhhhhh...eeeeee....hhhhhh....eeeeee.hhhhh........hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2l A   3 LITHFRQAIEETLPWLSSFGADPAGGMTRLLYSPEWLETQQQFKKRMAASGLETRFDEVGNLYGRLNGTEYPQEVVLSGSHIDTVVNGGNLDGQFGALAAWLAIDWLKTQYGAPLRTVEVVAMAEEEGSRFPYVFWGSKNIFGLANPDDVRNICDAKGNSFVDAMKACGFTLPNAPLTPRQDIKAFVELHIEQGCVLESNGQSIGVVNAIVGQRRYTVTLNGESNHAGTTPMGYRRDTVYAFSRICHQSVEKAKRMGDPLVLTFGKVEPRPNTVNVVPGKTTFTIDCRHTDAAVLRDFTQQLENDMRAICDEMDIGIDIDLWMDEEPVPMNKELVATLTELCEREKLNYRVMHSGAGHDAQIFAPRVPTCMIFIPSINGISHNPAERTNITDLAEGVKTLALMLYQLAWQK 413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 


Chain B from PDB  Type:PROTEIN  Length:410
 aligned with ALLC_ECOLI | P77425 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:410
                                    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       390       400       410
           ALLC_ECOLI     1 MITHFRQAIEETLPWLSSFGADPAGGMTRLLYSPEWLETQQQFKKRMAASGLETRFDEVGNLYGRLNGTEYPQEVVLSGSHIDTVVNGGNLDGQFGALAAWLAIDWLKTQYGAPLRTVEVVAMAEEEGSRFPYVFWGSKNIFGLANPDDVRNICDAKGNSFVDAMKACGFTLPNAPLTPRQDIKAFVELHIEQGCVLESNGQSIGVVNAIVGQRRYTVTLNGESNHAGTTPMGYRRDTVYAFSRICHQSVEKAKRMGDPLVLTFGKVEPRPNTVNVVPGKTTFTIDCRHTDAAVLRDFTQQLENDMRAICDEMDIGIDIDLWMDEEPVPMNKELVATLTELCEREKLNYRVMHSGAGHDAQIFAPRVPTCMIFIPSINGISHNPAERTNITDLAEGVKTLALMLYQLAWQ 410
               SCOP domains d1z2lb1 B:3-212,B:330-412 Allantoate amidohydrolase AllC catalytic domain                                                                                                                                         d1z2lb2 B:213-329 Allantoate amidohydrolase AllC                                                                     d1z2lb1 B:3-212,B:330-412 Allantoate amidohydrolase AllC catalytic domain           SCOP domains
               CATH domains 1z2lB01 B:3-213,B:329-412 Zn peptidases                                                                                                                                                                            1z2lB02 B:214-328  [code=3.30.70.360, no name defined]                                                             1z2lB01 B:3-213,B:329-412 Zn peptidases                                              CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------Peptidase_M20-1z2lB01 B:79-408                                                                                                                                                                                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------Peptidase_M20-1z2lB02 B:79-408                                                                                                                                                                                                                                                                                                            ---- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..eeee.....eeeee....eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhh...eeeeeeee...........hhhhhhhh...hhhhh.........hhhhhhhhh..............eeeeeeee....hhhhhh...eeeeeee.eeeeeeeeee...ee....hhhhh.hhhhhhhhhhhhhhhhhhhhh...eee...eeee.....ee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..ee.hhhhhhhhhhhhhhhh..eeeeee....hhhhhh....eeeee..hhhhh........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z2l B   3 LITHFRQAIEETLPWLSSFGADPAGGMTRLLYSPEWLETQQQFKKRMAASGLETRFDEVGNLYGRLNGTEYPQEVVLSGSHIDTVVNGGNLDGQFGALAAWLAIDWLKTQYGAPLRTVEVVAMAEEEGSRFPYVFWGSKNIFGLANPDDVRNICDAKGNSFVDAMKACGFTLPNAPLTPRQDIKAFVELHIEQGCVLESNGQSIGVVNAIVGQRRYTVTLNGESNHAGTTPMGYRRDTVYAFSRICHQSVEKAKRMGDPLVLTFGKVEPRPNTVNVVPGKTTFTIDCRHTDAAVLRDFTQQLENDMRAICDEMDIGIDIDLWMDEEPVPMNKELVATLTELCEREKLNYRVMHSGAGHDAQIFAPRVPTCMIFIPSINGISHNPAERTNITDLAEGVKTLALMLYQLAWQ 412
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
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: Peptidase_MH (119)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ALLC_ECOLI | P77425)
molecular function
    GO:0047652    allantoate deiminase activity    Catalysis of the reaction: allantoate + H2O + H+ = CO2 + NH3 + ureidoglycine.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016813    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amidine, a compound of the form R-C(=NH)-NH2.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0009442    allantoin assimilation pathway    The pathways by which allantoin is processed and converted to ureidoglycolate, and then into metabolically useful substrates. E. coli are able to utilize allantoin as a sole nitrogen source under anaerobic conditions by converting it to ureidoglycolate; this may be further metabolized to produce glyoxylate and thence 3-phosphoglycerate, or alternatively oxidized to oxolureate, which can converted into oxamate and carbamoylphosphate. This may then be further metabolized to CO2, NH4+ and ATP.
    GO:0000256    allantoin catabolic process    The chemical reactions and pathways resulting in the breakdown of allantoin, (2,5-dioxo-4-imidazolidinyl)urea.
    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:0006144    purine nucleobase metabolic process    The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.

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  1z2l
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALLC_ECOLI | P77425: 2imo 4pxd

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