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(-) Description

Title :  CRYSTAL STRUCTURE OF ALTRONATE HYDROLASE (FRAGMENT 1-84) FROM SHIGELLA FLEXNERI.
 
Authors :  J. Hou, M. Chruszcz, X. Xu, B. Le, M. D. Zimmerman, A. Savchenko, A. M. Edw A. Joachimiak, W. Minor, Midwest Center For Structural Genomics
Date :  04 Oct 09  (Deposition) - 27 Oct 09  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,H  (1x)
Biol. Unit 4:  F,G  (1x)
Keywords :  Altronate Hydrolase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hou, M. Chruszcz, X. Xu, B. Le, M. D. Zimmerman, A. Savchenko, A. M. Edwards, A. Joachimiak, W. Minor
Crystal Structure Of Altronate Hydrolase (Fragment 1-84) From Shigella Flexneri.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALTRONATE HYDROLASE
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-84
    Gene: S3338, SF3131, UXAA
    Organism Scientific: SHIGELLA FLEXNERI 2A STR. 2457T
    Organism Taxid: 198215

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A  D    
Biological Unit 2 (1x):  B  E   
Biological Unit 3 (1x):   C    H
Biological Unit 4 (1x):      FG 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CL3Ligand/IonCHLORIDE ION
3MLA2Ligand/IonMALONIC ACID
4MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MLA2Ligand/IonMALONIC ACID
4MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MLA-1Ligand/IonMALONIC ACID
4MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MLA-1Ligand/IonMALONIC ACID
4MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MLA-1Ligand/IonMALONIC ACID
4MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:43 , LYS A:57 , TYR A:58 , ILE A:62 , THR A:82 , HOH A:445 , HOH A:527 , MLA D:85 , HOH D:526BINDING SITE FOR RESIDUE MLA A 85
02AC2SOFTWARELYS B:43 , LYS B:57 , TYR B:58 , ILE B:62 , HOH B:597BINDING SITE FOR RESIDUE ACT B 85
03AC3SOFTWAREALA B:67 , ASP B:68BINDING SITE FOR RESIDUE CL B 86
04AC4SOFTWARELYS C:43 , LYS C:57 , TYR C:58 , ILE C:62 , THR C:82 , HOH C:285BINDING SITE FOR RESIDUE ACT C 85
05AC5SOFTWAREMLA A:85 , HOH A:527 , LYS D:43 , LYS D:57 , TYR D:58 , THR D:82 , HOH D:326 , HOH D:526BINDING SITE FOR RESIDUE MLA D 85
06AC6SOFTWARELYS E:43 , LYS E:57 , TYR E:58 , ILE E:62 , LEU E:84BINDING SITE FOR RESIDUE ACT E 85
07AC7SOFTWARELYS F:43 , LYS F:57 , TYR F:58 , ILE F:62 , THR F:82 , LEU F:84BINDING SITE FOR RESIDUE ACT F 85
08AC8SOFTWAREASP G:18BINDING SITE FOR RESIDUE CL G 85
09AC9SOFTWARELYS G:43 , LYS G:57 , TYR G:58 , ILE G:62BINDING SITE FOR RESIDUE ACT G 86
10BC1SOFTWAREARG H:40BINDING SITE FOR RESIDUE CL H 85
11BC2SOFTWARELYS H:43 , LYS H:57 , TYR H:58BINDING SITE FOR RESIDUE ACT H 86

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K3S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K3S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K3S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K3S)

(-) Exons   (0, 0)

(no "Exon" information available for 3K3S)

(-) 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:85
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:85
                             1                                                                                   
                             |       9        19        29        39        49        59        69        79     
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee........eeee..eeee.........eee........eeee..eeeeee........ee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3k3s A  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
                             |       9        19        29        39        49        59        69        79     
                             |                                                                                   
                             1-MSE                                                                               


Chain B from PDB  Type:PROTEIN  Length:85
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:85
                             1                                                                                   
                             |       9        19        29        39        49        59        69        79     
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee........eeee..eeee.........eee........eeee..eeeeee........ee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3k3s B  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
                             |       9        19        29        39        49        59        69        79     
                             1-MSE                                                                               


Chain C from PDB  Type:PROTEIN  Length:85
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:85
                             1                                                                                   
                             |       9        19        29        39        49        59        69        79     
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee........eeee..eeee.........eee........eeee..eeeeee........ee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3k3s C  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
                             |       9        19        29        39        49        59        69        79     
                             1-MSE                                                                               


Chain D from PDB  Type:PROTEIN  Length:85
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:85
                             1                                                                                   
                             |       9        19        29        39        49        59        69        79     
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee........eeee..eeee.........eee........eeee..eeeeee........ee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3k3s D  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
                             |       9        19        29        39        49        59        69        79     
                             1-MSE                                                                               


Chain E from PDB  Type:PROTEIN  Length:85
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:85
                             1                                                                                   
                             |       9        19        29        39        49        59        69        79     
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee........eeee..eeee.........eee........eeee..eeeeee........ee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3k3s E  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
                             |       9        19        29        39        49        59        69        79     
                             1-MSE                                                                               


Chain F from PDB  Type:PROTEIN  Length:85
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:85
                             1                                                                                   
                             |       9        19        29        39        49        59        69        79     
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee........eeee..eeee.........eee........eeee..eeeeee........ee....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3k3s F  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
                             |       9        19        29        39        49        59        69        79     
                             1-MSE                                                                               


Chain G from PDB  Type:PROTEIN  Length:85
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:85
                             1                                                                                   
                             |       9        19        29        39        49        59        69        79     
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeee........eeee..eeee.........eee........eeee..eeeeee........ee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                  3k3s G  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTNL 84
                             |       9        19        29        39        49        59        69        79     
                             1-MSE                                                                               


Chain H from PDB  Type:PROTEIN  Length:84
 aligned with Q83JJ2_SHIFL | Q83JJ2 from UniProtKB/TrEMBL  Length:495

    Alignment length:84
                             1                                                                                  
                             |       9        19        29        39        49        59        69        79    
          Q83JJ2_SHIFL    - -MQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTN 83
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------SAF-3k3sH01 H:10-81                                                     -- Pfam domains (1)
           Pfam domains (2) ----------SAF-3k3sH02 H:10-81                                                     -- Pfam domains (2)
           Pfam domains (3) ----------SAF-3k3sH03 H:10-81                                                     -- Pfam domains (3)
           Pfam domains (4) ----------SAF-3k3sH04 H:10-81                                                     -- Pfam domains (4)
           Pfam domains (5) ----------SAF-3k3sH05 H:10-81                                                     -- Pfam domains (5)
           Pfam domains (6) ----------SAF-3k3sH06 H:10-81                                                     -- Pfam domains (6)
           Pfam domains (7) ----------SAF-3k3sH07 H:10-81                                                     -- Pfam domains (7)
           Pfam domains (8) ----------SAF-3k3sH08 H:10-81                                                     -- Pfam domains (8)
         Sec.struct. author ...ee.......eeee........eee....eee.........eee........eeee..eeeeee........ee....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3k3s H  0 GmQYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLPIGYALADIAAGEHVHAHNTRTN 83
                             |       9        19        29        39        49        59        69        79    
                             1-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3K3S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K3S)

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: AFP_III-like (6)
(-)
Family: SAF (6)
(-)
Shigella flexneri (1)
1aSAF-3k3sH01H:10-81
1bSAF-3k3sH02H:10-81
1cSAF-3k3sH03H:10-81
1dSAF-3k3sH04H:10-81
1eSAF-3k3sH05H:10-81
1fSAF-3k3sH06H:10-81
1gSAF-3k3sH07H:10-81
1hSAF-3k3sH08H:10-81

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (Q83JJ2_SHIFL | Q83JJ2)
molecular function
    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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

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