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(-) Description

Title :  CRYSTAL STRUCTURE OF CHITINASE A MUTANT E315Q COMPLEXED WITH OCTA-N-ACETYLCHITOOCTAOSE (NAG)8.
 
Authors :  Y. Papanikolau, G. Prag, G. Tavlas, C. E. Vorgias, A. B. Oppenheim, K. Pe
Date :  22 Feb 00  (Deposition) - 22 Feb 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Protein-Oligosaccharide Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Papanikolau, G. Prag, G. Tavlas, C. E. Vorgias, A. B. Oppenheim, K. Petratos
High Resolution Structural Analyses Of Mutant Chitinase A Complexes With Substrates Provide New Insight Into The Mechanism Of Catalysis.
Biochemistry V. 40 11338 2001
PubMed-ID: 11560481  |  Reference-DOI: 10.1021/BI010505H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITINASE A
    Chains: A
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBR322
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARENAG A:2 , TYR A:170 , PHE A:232 , LYS A:237 , HOH A:1344 , HOH A:1345 , HOH A:1346 , HOH A:1348BINDING SITE FOR RESIDUE NAG A 1
2AC2SOFTWARENAG A:1 , NAG A:3 , ASN A:70 , TYR A:170 , HOH A:1347 , HOH A:1348BINDING SITE FOR RESIDUE NAG A 2
3AC3SOFTWARENAG A:2 , NAG A:4 , TRP A:167 , ARG A:172 , HOH A:836 , HOH A:892 , HOH A:1349 , HOH A:1351 , HOH A:1352 , HOH A:1353BINDING SITE FOR RESIDUE NAG A 3
4AC4SOFTWARENAG A:3 , NAG A:5 , TRP A:167 , ARG A:172 , THR A:276 , GLU A:473 , HOH A:892 , HOH A:1355BINDING SITE FOR RESIDUE NAG A 4
5AC5SOFTWARENAG A:4 , NAG A:6 , TRP A:275 , THR A:276 , GLU A:473 , TRP A:539 , GLU A:540 , HOH A:1320 , HOH A:1356 , HOH A:1357 , HOH A:1358 , HOH A:1363BINDING SITE FOR RESIDUE NAG A 5
6AC6SOFTWARENAG A:5 , NAG A:7 , TYR A:163 , TRP A:275 , ASP A:313 , GLN A:315 , ALA A:362 , MET A:388 , TYR A:390 , ASP A:391 , TYR A:444 , ARG A:446 , TRP A:539 , HOH A:1359 , HOH A:1363BINDING SITE FOR RESIDUE NAG A 6
7AC7SOFTWARENAG A:6 , NAG A:8 , TRP A:275 , GLN A:315 , PHE A:316 , ASP A:391 , ARG A:446 , HOH A:1126 , HOH A:1360 , HOH A:1362 , HOH A:1363BINDING SITE FOR RESIDUE NAG A 7
8AC8SOFTWARENAG A:7 , TRP A:275 , LYS A:369 , ASP A:391 , PHE A:396 , TYR A:418 , HOH A:1169 , HOH A:1364 , HOH A:1365 , HOH A:1366 , HOH A:1367 , HOH A:1368 , HOH A:1369BINDING SITE FOR RESIDUE NAG A 8

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:115 -A:120
2A:195 -A:218

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:190 -Phe A:191
2Gln A:315 -Phe A:316
3Trp A:539 -Glu A:540

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA_SERMA307-315  1A:307-314

(-) Exons   (0, 0)

(no "Exon" information available for 1EHN)

(-) 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:540
 aligned with CHIA_SERMA | P07254 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:540
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563
           CHIA_SERMA    24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDAGTTAKILLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSAETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGPFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKVVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWKNGIVDYRQIAGQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAGVQ 563
               SCOP domains d1ehna1 A:24-132 Chitinase A, N-terminal domain N                                                            d1ehna2 A:133-443,A:517-563 Chitinase A, catalytic domain                                                                                                                                                                                                                                                              d1ehna3 A:444-516 Chitinase A                                            d1ehna2 A:133-443,A:517-563                     SCOP domains
               CATH domains 1ehnA01 A:24-130 Immunoglobulins                                                                           1ehnA02 A:131-442,A:519-561 Glycosidases                                                                                                                                                                                                                                                                                1ehnA03 A:443-518  [code=3.10.50.10, no name defined]                       1ehnA02 A:131-442,A:519-561 Glycosidases   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee.....eee.eee.....hhhhheee...eeeeeeee........eeeeee..eeeeeee....eeeeeeee...eeeeeeeeeee..eeee...eeeeee...........................eeeeeee.hhhh....hhhhhhhhhh.eeeeeee........hhhhhhh.hhhhhhhhhh...........hhhhhhh.............hhhhhhhhhhhhhh...eeeeeee....hhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeee................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh..hhhhhhhhh.eeeee..............................hhhhhhhhhhhhh.hhh.eeeeee.eeeeee........hhhhh...ee........eeehhhhhhhh.....eeeee....eeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHITINASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ehn A  24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDTGTTAKVLLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWQFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSVETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENGIVDYRQIAGQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAGVQ 563
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EHN)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHIA_SERMA | P07254)
molecular function
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    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:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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  3.2.1.14
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHIA_SERMA | P07254: 1ctn 1eib 1ffq 1ffr 1k9t 1nh6 1rd6 1x6l 1x6n 2wk2 2wly 2wlz 2wm0

(-) Related Entries Specified in the PDB File

1ctn 1CTN CONTAINS THE NATIVE PROTEIN AT 2.3 ANGSTROM RESOLUTION
1edq 1EDQ CONTAINS THE NATIVE PROTEIN AT 1.55 ANGSTROM RESOLUTION
1eib 1EIB CONTAINS THE D313A MUTANT COMPLEXED WITH OCTA-N- ACETYLCHITOOCTAOSE AT 1.8 ANGSTROM RESOLUTION