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The Open Protein Structure Annotation Network
PDB Keyword
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3lmz

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Putative sugar isomerase. (YP_001305105.1) from Parabacteroides distasonis ATCC 8503 at 1.44 A resolution. To be published
    Site JCSG
    PDB Id 3lmz Target Id 396625
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS27956,YP_001305105.1, PF07582, 327056 Molecular Weight 29024.88 Da.
    Residues 256 Isoelectric Point 6.06
    Sequence alpdpvkpkapkavnpfhlgmagytfvnfdldttlktlerldihylcikdfhlplnstdeqirafhdkc aahkvtgyavgpiymkseeeidrafdyakrvgvklivgvpnyellpyvdkkvkeydfhyaihlhgpdik typdatdvwvhtkdldprigmcldvghdlrngcdpvadlkkyhtrvfdmhikdvtdsskagvgieigrg kidfpalirmmrevnytgmcsleyekdmkdpflgiaesigyfkavsdlt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.44 Rfree 0.185
    Matthews' coefficent 2.60 Rfactor 0.149
    Waters 419 Solvent Content 52.77

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam update:This structure is clearly a member of the AP endonuclease/Xylose Isomerase TIM barrel family (PF01261).

    Gene BDI_3797 from  Parabacteroides distasonis atcc 8503 encodes the YP_001305105.1 amino acid sequence of a putative uncharaterized protein containing a classic TIM barrel fold. It belongs to the xylose isomerase-like TIM barrel group (PF01261).

    SCOP classifies 3lmz in the alpha/beta class, xylose isomerase-like superfamily, IolI-like family. There is only one molecule found in the asu. However, PISA predicts a dimer as a biomolecule.

     

    A.png

     Fig 1. 3lmz structure as seen in the asu.

      

    DALI hits using 3lmz as query includes sugar epimerases as top hits:

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 2zds-B 25.2 2.1 233 322 18 PDB MOLECULE: PUTATIVE DNA-BINDING PROTEIN; 2: 2zds-A 25.1 2.0 232 321 17 PDB MOLECULE: PUTATIVE DNA-BINDING PROTEIN; 3: 2zds-C 25.1 2.2 234 322 17 PDB MOLECULE: PUTATIVE DNA-BINDING PROTEIN; 4: 2zds-F 25.0 2.2 234 322 17 PDB MOLECULE: PUTATIVE DNA-BINDING PROTEIN; 5: 2zds-E 25.0 2.2 234 321 17 PDB MOLECULE: PUTATIVE DNA-BINDING PROTEIN; 6: 2zds-D 25.0 2.2 234 322 17 PDB MOLECULE: PUTATIVE DNA-BINDING PROTEIN; 7: 3cqj-B 24.7 2.5 231 275 16 PDB MOLECULE: L-RIBULOSE-5-PHOSPHATE 3-EPIMERASE ULAE; 8: 3cqi-A 24.5 2.6 233 277 16 PDB MOLECULE: L-RIBULOSE-5-PHOSPHATE 3-EPIMERASE ULAE; 9: 3cqj-A 24.5 2.5 232 276 16 PDB MOLECULE: L-RIBULOSE-5-PHOSPHATE 3-EPIMERASE ULAE; 10: 3cqk-A 24.5 2.5 231 276 16 PDB MOLECULE: L-RIBULOSE-5-PHOSPHATE 3-EPIMERASE ULAE; 11: 3cqk-B 24.4 2.5 231 276 16 PDB MOLECULE: L-RIBULOSE-5-PHOSPHATE 3-EPIMERASE ULAE; 12: 3cqi-B 24.3 2.5 228 273 16 PDB MOLECULE: L-RIBULOSE-5-PHOSPHATE 3-EPIMERASE ULAE; 13: 1i6n-A 23.8 2.9 236 278 20 PDB MOLECULE: IOLI PROTEIN; 14: 1i60-A 23.5 3.1 238 278 20 PDB MOLECULE: IOLI PROTEIN; 15: 3cny-B 23.5 2.7 234 300 18 PDB MOLECULE: INOSITOL CATABOLISM PROTEIN IOLE; 16: 2zvr-B 23.4 2.4 225 262 14 PDB MOLECULE: UNCHARACTERIZED PROTEIN TM_0416; 17: 3cny-A 23.3 2.7 233 300 18 PDB MOLECULE: INOSITOL CATABOLISM PROTEIN IOLE; 18: 3dx5-A 23.2 2.6 228 274 11 PDB MOLECULE: UNCHARACTERIZED PROTEIN ASBF; 19: 3ktc-A 23.1 2.5 233 330 15 PDB MOLECULE: XYLOSE ISOMERASE; 20: 3ktc-B 23.0 2.5 233 330 15 PDB MOLECULE: XYLOSE ISOMERASE; 21: 2zvr-A 22.9 2.4 220 259 14 PDB MOLECULE: UNCHARACTERIZED PROTEIN TM_0416; 22: 2qum-C 22.8 2.6 226 290 16 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 23: 1xih 22.7 2.6 235 385 15 PDB D-XYLOSE ISOMERASE (E.C.5.3.1.5) COMPLEXED WITH D-SORBITOL 24: 2qul-C 22.7 2.6 226 290 15 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 25: 2qum-D 22.7 2.6 226 290 15 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 26: 1oad-A 22.7 2.6 234 387 15 PDB MOLECULE: XYLOSE ISOMERASE; 27: 1xih-A 22.7 2.6 235 385 15 PDB MOLECULE: D-XYLOSE ISOMERASE; 28: 2qum-A 22.7 2.6 226 290 15 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 29: 2qul-B 22.7 2.6 226 290 15 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 30: 2qum-B 22.7 2.6 226 290 16 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 31: 1s5n-A 22.7 2.7 236 386 17 PDB MOLECULE: XYLOSE ISOMERASE; 32: 1s5m-A 22.7 2.7 235 386 17 PDB MOLECULE: XYLOSE ISOMERASE; 33: 2gub-A 22.7 2.6 235 385 15 PDB MOLECULE: XYLOSE ISOMERASE; 34: 1xlc-B 22.6 2.7 234 393 13 PDB MOLECULE: D-XYLOSE ISOMERASE; 35: 1xlh-B 22.6 2.7 234 393 13 PDB MOLECULE: D-XYLOSE ISOMERASE; 36: 1xlg-B 22.6 2.6 234 393 13 PDB MOLECULE: D-XYLOSE ISOMERASE; 37: 1xli-B 22.6 2.7 234 393 13 PDB MOLECULE: D-XYLOSE ISOMERASE; 38: 1xlb-B 22.6 2.7 234 393 13 PDB MOLECULE: D-XYLOSE ISOMERASE; 39: 1xif 22.6 2.6 234 388 15 PDB D-XYLOSE ISOMERASE (E.C.5.3.1.5) COMPLEXED WITH GLUCOSE, 40: 2gyi-A 22.6 2.6 235 385 17 PDB MOLECULE: XYLOSE ISOMERASE; 41: 1xic 22.6 2.6 235 385 15 PDB D-XYLOSE ISOMERASE (E.C.5.3.1.5) COMPLEXED WITH D-XYLOSE 42: 1xyb-A 22.6 2.7 235 386 17 PDB MOLECULE: XYLOSE ISOMERASE; 43: 2gve-A 22.6 2.6 234 388 15 PDB MOLECULE: XYLOSE ISOMERASE; 44: 1xif-A 22.6 2.6 235 388 15 PDB MOLECULE: D-XYLOSE ISOMERASE; 45: 1o1h-A 22.6 2.6 234 386 15 PDB MOLECULE: XYLOSE ISOMERASE; 46: 1xic-A 22.6 2.6 235 385 15 PDB MOLECULE: D-XYLOSE ISOMERASE; 47: 1o1h-B 22.6 2.7 234 386 15 PDB MOLECULE: XYLOSE ISOMERASE; 48: 2qul-D 22.6 2.6 226 290 15 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 49: 2qul-A 22.6 2.6 226 290 15 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE; 50: 2ou4-A 22.5 2.6 226 290 15 PDB MOLECULE: D-TAGATOSE 3-EPIMERASE;

     

     Superposition of 3lmz (green) with 2zds (left, yelllow) and with 3cny (right, purple) are shown below.

    A_2ds.pngA_3cny.png

    Interestingly, the putative active site residue (His158, green) of 3lmz is converved as

    His159 in 3cny (purple) structure as shown below.

    A citric acid molecule (CIT) is also found in the putative active site of 3lmz (green).

     

    super_HIs159_3cny.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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