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(-) Description

Title :  YCDX PROTEIN IN AUTOINHIBITED STATE
 
Authors :  A. Teplyakov, G. Obmolova, P. P. Khil, R. D. Camerini-Otero, G. L. Gilliland
Date :  14 May 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Beta-Alpha-Barrel, Trinuclear Zinc, Autoinhibition, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Teplyakov, G. Obmolova, P. P. Khil, R. D. Camerini-Otero, G. L. Gilliland
Autoregulation Of Ycdx Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YCDX
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YCDX
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2SO44Ligand/IonSULFATE ION
3ZN9Ligand/IonZINC ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:15 , HIS A:40 , HIS A:164 , HIS A:194BINDING SITE FOR RESIDUE ZN A 1301
02AC2SOFTWAREHIS A:7 , HIS A:9 , GLU A:73 , ASP A:192 , ZN A:1303 , HOH A:1334BINDING SITE FOR RESIDUE ZN A 1302
03AC3SOFTWAREGLU A:73 , HIS A:101 , HIS A:131 , ZN A:1302 , HOH A:1334BINDING SITE FOR RESIDUE ZN A 1303
04AC4SOFTWAREHIS B:15 , HIS B:40 , HIS B:164 , HIS B:194BINDING SITE FOR RESIDUE ZN B 1311
05AC5SOFTWAREHIS B:7 , HIS B:9 , GLU B:73 , ASP B:192 , ZN B:1313 , HOH B:1399BINDING SITE FOR RESIDUE ZN B 1312
06AC6SOFTWAREGLU B:73 , HIS B:101 , HIS B:131 , ZN B:1312 , HOH B:1399BINDING SITE FOR RESIDUE ZN B 1313
07AC7SOFTWAREHIS C:15 , HIS C:40 , HIS C:164 , HIS C:194BINDING SITE FOR RESIDUE ZN C 1321
08AC8SOFTWAREHIS C:7 , HIS C:9 , GLU C:73 , ASP C:192 , ZN C:1323 , HOH C:1354BINDING SITE FOR RESIDUE ZN C 1322
09AC9SOFTWAREGLU C:73 , HIS C:101 , HIS C:131 , ZN C:1322 , HOH C:1354BINDING SITE FOR RESIDUE ZN C 1323
10BC1SOFTWAREGLN A:152 , TRP A:186 , ARG A:218 , HOH A:1348 , HOH A:1439 , HOH A:1532BINDING SITE FOR RESIDUE SO4 A 1324
11BC2SOFTWAREGLN B:152 , TRP B:186 , ARG B:218 , HOH B:1341 , HOH B:1452 , HOH B:1456BINDING SITE FOR RESIDUE SO4 B 1334
12BC3SOFTWAREGLN C:152 , TRP C:186 , ARG C:218 , HOH C:1348 , HOH C:1412 , HOH C:1465 , HOH C:1471BINDING SITE FOR RESIDUE SO4 C 1344
13BC4SOFTWAREARG A:70 , HOH A:1376 , HOH A:1416 , HOH A:1504BINDING SITE FOR RESIDUE SO4 A 1305
14BC5SOFTWAREARG A:61 , VAL A:62 , HOH A:1502BINDING SITE FOR RESIDUE FMT A 1306
15BC6SOFTWAREPRO B:60 , ARG B:61 , VAL B:62 , HOH B:1391BINDING SITE FOR RESIDUE FMT B 1326
16BC7SOFTWAREPRO C:60 , ARG C:61 , VAL C:62 , HOH C:1433 , HOH C:1595BINDING SITE FOR RESIDUE FMT C 1336
17BC8SOFTWAREARG B:181 , VAL B:212BINDING SITE FOR RESIDUE FMT B 1307
18BC9SOFTWAREARG C:181 , HOH C:1540BINDING SITE FOR RESIDUE FMT C 1317
19CC1SOFTWAREARG B:70 , HOH B:1453 , HOH B:1492BINDING SITE FOR RESIDUE FMT B 1318

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PB0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PB0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PB0)

(-) Exons   (0, 0)

(no "Exon" information available for 1PB0)

(-) 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:236
 aligned with YCDX_ECOLI | P75914 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           YCDX_ECOLI     1 MYPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEINNSSFLHSRKGSEDNCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
               SCOP domains d1pb0a_ A: Hypothetical protein YcdX                                                                                                                                                                                                                  SCOP domains
               CATH domains 1pb0A00 A:1-245 Metal-dependent hydrolases                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.............hhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhh..ee..eeeeeeeeee..........hhhhhhhh.eeeee.........hhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhh..eeee.---....------hhhhhhhhhhhhh..eee.....hhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pb0 A   1 MYPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEIN---FLHS------NCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       | - |  |    - |     180       190       200       210       220       230       240     
                                                                                                                                                                                       158 162  |    172                                                                         
                                                                                                                                                                                              165                                                                                


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with YCDX_ECOLI | P75914 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           YCDX_ECOLI     1 MYPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEINNSSFLHSRKGSEDNCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
               SCOP domains d1pb0b_ B: Hypothetical protein YcdX                                                                                                                                                                                                                  SCOP domains
               CATH domains 1pb0B00 B:1-245 Metal-dependent hydrolases                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.............hhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhh..ee..eeeeeeeeee..........hhhhhhhh.eeeee.........hhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhh..eeee.---...-------hhhhhhhhhhhhh..eee.....hhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pb0 B   1 MYPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEIN---FLH-------NCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       | - | |     - |     180       190       200       210       220       230       240     
                                                                                                                                                                                       158 162 |     172                                                                         
                                                                                                                                                                                             164                                                                                 


Chain C from PDB  Type:PROTEIN  Length:235
 aligned with YCDX_ECOLI | P75914 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
           YCDX_ECOLI     1 MYPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEINNSSFLHSRKGSEDNCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
               SCOP domains d1pb0c_ C: Hypothetical protein YcdX                                                                                                                                                                                                                  SCOP domains
               CATH domains 1pb0C00 C:1-245 Metal-dependent hydrolases                                                                                                                                                                                                            CATH domains
           Pfam domains (1) ---PHP-1pb0C01 C:4-175                                                                                                                                                         ---------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---PHP-1pb0C02 C:4-175                                                                                                                                                         ---------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---PHP-1pb0C03 C:4-175                                                                                                                                                         ---------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ...ee.............hhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhh..ee..eeeeeeeeee..........hhhhhhhh.eeeee.........hhhhhhhhhhhhhh.....ee..........hhhhhhhhhhhh..eeee.---...-------hhhhhhhhhhhhh..eee.....hhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pb0 C   1 MYPVDLHMHTVASTHAYSTLSDYIAQAKQKGIKLFAITDHGPDMEDAPHHWHFINMRIWPRVVDGVGILRGIEANIKNVDGEIDCSGKMFDSLDLIIAGFHEPVFAPHDKATNTQAMIATIASGNVHIISHPGNPKYEIDVKAVAEAAAKHQVALEIN---FLH-------NCREVAAAVRDAGGWVALGSDSHTAFTMGEFEECLKILDAVDFPPERILNVSPRRLLNFLESRGMAPIAEFADL 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       | - | |     - |     180       190       200       210       220       230       240     
                                                                                                                                                                                       158 162 |     172                                                                         
                                                                                                                                                                                             164
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (YCDX_ECOLI | P75914)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0042578    phosphoric ester hydrolase activity    Catalysis of the reaction: RPO-R' + H2O = RPOOH + R'H. This reaction is the hydrolysis of any phosphoric ester bond, any ester formed from orthophosphoric acid, O=P(OH)3.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0071978    bacterial-type flagellum-dependent swarming motility    Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    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
        YCDX_ECOLI | P75914: 1m65 1m68

(-) Related Entries Specified in the PDB File

1m65 YCDX PROTEIN, ONE ZINC ION PER SUBUNIT, TRIGONAL CRYSTAL FORM
1m68 YCDX PROTEIN, THREE ZINC IONS PER SUBUNIT, TRIGONAL CRYSTAL FORM