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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE (YP_676759.1) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Nov 09  (Deposition) - 17 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Putative Phosphoribosylformylglycinamidine Cyclo-Ligase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (Yp_676759. 1 From Cytophaga Hutchinsonii Atcc 33406 At 1. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
    Chains: A, B
    EC Number: 6.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PURM, CHU_0126
    Organism Scientific: CYTOPHAGA HUTCHINSONII ATCC 33406
    Organism Taxid: 269798
    Strain: ATCC 33406 / NCIMB 9469

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 33)

Asymmetric/Biological Unit (3, 33)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:106 , GLY A:146 , GLU A:147 , THR A:148BINDING SITE FOR RESIDUE ACT A 394
02AC2SOFTWARELYS A:28 , TYR A:31 , PRO A:32 , ALA A:34 , LYS A:37BINDING SITE FOR RESIDUE ACT A 395
03AC3SOFTWAREPHE A:35 , HIS A:54 , ASP A:92 , LYS A:295 , PHE A:299 , HOH A:694BINDING SITE FOR RESIDUE ACT A 396
04AC4SOFTWAREILE A:174 , LYS A:279 , GLY A:280 , LYS A:281 , LEU A:282 , HOH A:660 , HOH A:712BINDING SITE FOR RESIDUE EDO A 397
05AC5SOFTWAREASP A:56 , GLY A:57 , MSE A:88 , SER A:206 , HOH A:578BINDING SITE FOR RESIDUE EDO A 398
06AC6SOFTWAREGLU A:118 , ASP A:309 , ILE A:367 , GLY A:369 , ARG A:370 , HOH A:416 , HOH A:425BINDING SITE FOR RESIDUE EDO A 399
07AC7SOFTWAREGLN A:277 , ASP B:100 , GLY B:138 , LYS B:272BINDING SITE FOR RESIDUE ACT B 394
08AC8SOFTWAREILE B:30 , TYR B:31 , ARG B:170 , GLU B:235 , ASN B:236 , HOH B:596 , HOH B:694BINDING SITE FOR RESIDUE EDO B 395
09AC9SOFTWAREGLY A:377 , THR A:391 , ALA A:393 , GLN B:193 , HOH B:423 , HOH B:891BINDING SITE FOR RESIDUE EDO B 396
10BC1SOFTWARETRP B:69 , GLY B:73 , ILE B:75 , GLU B:118 , ARG B:370 , GLU B:372 , HOH B:558 , HOH B:571 , HOH B:579BINDING SITE FOR RESIDUE EDO B 397
11BC2SOFTWAREASP B:56 , GLY B:57 , MSE B:88 , SER B:206 , HOH B:725 , HOH B:876BINDING SITE FOR RESIDUE EDO B 398
12BC3SOFTWAREGLU B:118 , ASP B:309 , ILE B:367 , GLY B:369 , ARG B:370 , HOH B:546 , HOH B:744BINDING SITE FOR RESIDUE EDO B 399
13BC4SOFTWAREPHE B:35 , HIS B:54 , ASP B:92 , LYS B:295 , HOH B:647BINDING SITE FOR RESIDUE EDO B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KIZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KIZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KIZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KIZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3KIZ)

(-) 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:367
 aligned with Q11YU7_CYTH3 | Q11YU7 from UniProtKB/TrEMBL  Length:393

    Alignment length:367
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       
         Q11YU7_CYTH3    27 DKGIYPRAFCKIIPDILGGDPEYCNIMHADGAGTKSSLAYVYWKETGDISVWKGIAQDAVIMNIDDLICVGAVDNILLSSTIGRNKNLIPGEVLAAIINGTEEVLQMLRDNGIGIYSTGGETADVGDLVRTIIVDSTVTCRMKRQDVISNENIKAGNVIVGFASYGQTSYETEYNGGMGSNGLTSARHDVFNNVLASKYPESFDPKVPENLVYSGEMNLTDPYLNVPLDAGKLVLSPTRTYAPLMKEIIHQYKGKLDGVVHCSGGGQTKVLHFTDATTHIIKDNLFDVPPLFQLIQGQSNTPWEEMYKVFNMGHRLEIYTDAAHAEGMIAIAKKFNIEAKIIGRVEAPVAGKRLTITGPQGTEYTYA 393
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............ee........eeeeeeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......eeeeeeeeeeee.hhh.hhhhh....eeeeee..................hhhhhhhhhh.hhhhhhhhhhh....hhhhh................hhhhhhhh....hhhhhhhhhhhh.....eeee...hhhhhhhhhh....eeee......hhhhhhhhhhhh.hhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh...eeeeeeee.......eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kiz A  27 DKGIYPRAFCKIIPDILGGDPEYCNImHADGAGTKSSLAYVYWKETGDISVWKGIAQDAVImNIDDLICVGAVDNILLSSTIGRNKNLIPGEVLAAIINGTEEVLQmLRDNGIGIYSTGGETADVGDLVRTIIVDSTVTCRmKRQDVISNENIKAGNVIVGFASYGQTSYETEYNGGmGSNGLTSARHDVFNNVLASKYPESFDPKVPENLVYSGEmNLTDPYLNVPLDAGKLVLSPTRTYAPLmKEIIHQYKGKLDGVVHCSGGGQTKVLHFTDATTHIIKDNLFDVPPLFQLIQGQSNTPWEEmYKVFNmGHRLEIYTDAAHAEGmIAIAKKFNIEAKIIGRVEAPVAGKRLTITGPQGTEYTYA 393
                                    36        46      | 56        66        76        86 |      96       106       116       126      |136       146       156       166 |     176       186       196       206       216       226       236      |246       256       266    |  276       286       296       306       316       326     | 336 |     346       356       366       376       386       
                                                     53-MSE                             88-MSE                                      133-MSE                            168-MSE                             204-MSE                                243-MSE                     271-MSE                                                      332-MSE |             354-MSE                                   
                                                                                                                                                                                                                                                                                                                                                 338-MSE                                                   


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with Q11YU7_CYTH3 | Q11YU7 from UniProtKB/TrEMBL  Length:393

    Alignment length:371
                                    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 
         Q11YU7_CYTH3    23 IKSIDKGIYPRAFCKIIPDILGGDPEYCNIMHADGAGTKSSLAYVYWKETGDISVWKGIAQDAVIMNIDDLICVGAVDNILLSSTIGRNKNLIPGEVLAAIINGTEEVLQMLRDNGIGIYSTGGETADVGDLVRTIIVDSTVTCRMKRQDVISNENIKAGNVIVGFASYGQTSYETEYNGGMGSNGLTSARHDVFNNVLASKYPESFDPKVPENLVYSGEMNLTDPYLNVPLDAGKLVLSPTRTYAPLMKEIIHQYKGKLDGVVHCSGGGQTKVLHFTDATTHIIKDNLFDVPPLFQLIQGQSNTPWEEMYKVFNMGHRLEIYTDAAHAEGMIAIAKKFNIEAKIIGRVEAPVAGKRLTITGPQGTEYTYA 393
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------AIRS_C-3kizB01 B:180-379                                                                                                                                                                                -------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------AIRS_C-3kizB02 B:180-379                                                                                                                                                                                -------------- Pfam domains (2)
         Sec.struct. author hhhhhhh.........ee........eeeeeeeee..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.......eeeeeeeeeeee.hhh.hhhhh....eeeeee..................hhhhhhhhhh.hhhhhhhhhhh....hhhhh................hhhhhhhh....hhhhhhhhhhhhh..eeeeee...hhhhhhhhhh....eeee......hhhhhhhhhhhh.hhhhhhhhh...eeeeeeehhhhhhhhhhhhhhh...eeeeeeee.......eeee.....eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kiz B  23 IKSIDKGIYPRAFCKIIPDILGGDPEYCNImHADGAGTKSSLAYVYWKETGDISVWKGIAQDAVImNIDDLICVGAVDNILLSSTIGRNKNLIPGEVLAAIINGTEEVLQmLRDNGIGIYSTGGETADVGDLVRTIIVDSTVTCRmKRQDVISNENIKAGNVIVGFASYGQTSYETEYNGGmGSNGLTSARHDVFNNVLASKYPESFDPKVPENLVYSGEmNLTDPYLNVPLDAGKLVLSPTRTYAPLmKEIIHQYKGKLDGVVHCSGGGQTKVLHFTDATTHIIKDNLFDVPPLFQLIQGQSNTPWEEmYKVFNmGHRLEIYTDAAHAEGmIAIAKKFNIEAKIIGRVEAPVAGKRLTITGPQGTEYTYA 393
                                    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 
                                                         53-MSE                             88-MSE                                      133-MSE                            168-MSE                             204-MSE                                243-MSE                     271-MSE                                                      332-MSE |             354-MSE                                   
                                                                                                                                                                                                                                                                                                                                                     338-MSE
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3KIZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KIZ)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: AIRS_C] (13)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q11YU7_CYTH3 | Q11YU7)
molecular function
    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:0004641    phosphoribosylformylglycinamidine cyclo-ligase activity    Catalysis of the reaction: 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-D-ribosyl)imidazole + ADP + 2 H(+) + phosphate.

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